System OS: Windows 10, Architecture: AMD64
Java Info: 1.8.0_152, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation


Version info:
FragPipe version 17.1
MSFragger version 3.4
Philosopher version 4.1.0 (build 1635640020)


LCMS files:
  Experiment/Group: 
  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.mzXML	DIA
  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.mzXML	DIA
  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.mzXML	DIA
  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.mzXML	DIA
  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.mzXML	DIA
  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.mzXML	DIA
  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.mzXML	DIA
  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.mzXML	DIA
  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.mzXML	DIA


310 commands to execute:
CheckCentroid
java -Xmx25G -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" com.dmtavt.fragpipe.util.CheckCentroid C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.mzXML 7
WorkspaceCleanInit [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
WorkspaceCleanInit [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mgf
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mgf
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mgf
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mgf
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mgf
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mgf
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mgf
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mgf
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Peak
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.DIAWindowsFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.RTidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q1
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q2
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q3
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanidxFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanPosFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanRTFS
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_diasetting.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_params.ser
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mgf
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mgf
MSFragger [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
java -jar -Dfile.encoding=UTF-8 -Xmx25G C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\MSFragger-3.4.jar C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\fragger_dda.params C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML
PeptideProphet [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Users\jossmith\MSFragger\Philosopher\2020-02-03-decoys-reviewed-contam-UP000005640.fas --combine JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.pepXML
Rewrite pepxml [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML
ProteinProphet [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\filelist_proteinprophet.txt
PhilosopherDbAnnotate [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\jossmith\MSFragger\Philosopher\2020-02-03-decoys-reviewed-contam-UP000005640.fas --prefix rev_
PhilosopherFilter [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe filter --sequential --mapmods --prot 0.01 --tag rev_ --pepxml C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger --protxml C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\combined.prot.xml --razor
PhilosopherReport [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe report --decoys
SpecLibGen [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\Python\python -u C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\speclib\gen_con_spec_lib.py C:\Users\jossmith\MSFragger\Philosopher\2020-02-03-decoys-reviewed-contam-UP000005640.fas C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger unused C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger True unused use_easypqp noiRT;noIM 7 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.1" delete_intermediate_files C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\filelist_speclibgen.txt
PTMShepherd [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
java -Xmx25G -Dbatmass.io.libs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\ptmshepherd-1.2.6.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\shepherd.config"
WorkspaceClean [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
~~~~~~~~~~~~~~~~~~~~~~

Execution order:

    Cmd: [START], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [CheckCentroid], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [UmpireSe], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [MSFragger], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [PeptideProphet], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [ProteinProphet], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [PhilosopherDbAnnotate], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [PhilosopherFilter], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [PhilosopherReport], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [SpecLibGen], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [PTMShepherd], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
    Cmd: [WorkspaceClean], Work dir: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]

~~~~~~~~~~~~~~~~~~~~~~
~~~~~~~~~ fragpipe.config ~~~~~~~~~
# FragPipe v17.1ui state cache

AdjustFragIntensity=true
BoostComplementaryIon=false
CorrThreshold=0.1
DeltaApex=0.1
ExportPrecursorPeak=true
RFmax=500
RPmax=50
RTOverlap=0.3
SE.EstimateBG=false
SE.IsoPattern=0.3
SE.MS1PPM=10
SE.MS2PPM=20
SE.MS2SN=1.1
SE.MassDefectFilter=false
SE.MassDefectOffset=0.1
SE.MaxCurveRTRange=1
SE.MaxNoPeakCluster=6
SE.MinFrag=10
SE.MinMSIntensity=1
SE.MinMSMSIntensity=1
SE.MinNoPeakCluster=2
SE.NoMissedScan=2
SE.SN=1.1
WindowSize=6
crystalc.run-crystalc=false
database.db-path=C\:\\Users\\jossmith\\MSFragger\\Philosopher\\2020-02-03-decoys-reviewed-contam-UP000005640.fas
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=0
diann.run-dia-nn=false
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=10
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=false
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=true
diaumpire_se.params=C\:\\Users\\jossmith\\MSFragger\\DIA-Umpire\\umpire-se_Nesviz_Config_022421.txt
fragpipe-config.bin-msfragger=C\:\\Users\\jossmith\\MSFragger\\FragPipe-17.1\\fragpipe\\tools\\MSFragger-3.4\\MSFragger-3.4.jar
fragpipe-config.bin-philosopher=C\:\\Users\\jossmith\\MSFragger\\FragPipe-17.1\\fragpipe\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\jossmith\\Python\\python
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=true
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.locprob=0.75
ionquant.maxlfq=1
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0.5
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=1
ionquant.minisotopes=1
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=0.01
ionquant.proteinfdr=0.01
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=false
ionquant.tp=3
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=false
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=30
msfragger.digest_min_length=5
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=10
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=trypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=tsv_pepXML
msfragger.output_max_expect=10
msfragger.output_report_topN=2
msfragger.override_charge=false
msfragger.precursor_mass_lower=-150
msfragger.precursor_mass_mode=corrected
msfragger.precursor_mass_units=0
msfragger.precursor_mass_upper=500
msfragger.precursor_true_tolerance=10
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=CHKYWST
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name=trypsin
msfragger.search_enzyme_name_1=trypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=P
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.000000,C-Term Peptide,true,-1; 0.000000,N-Term Peptide,true,-1; 0.000000,C-Term Protein,true,-1; 0.000000,N-Term Protein,true,-1; 0.000000,G (glycine),true,-1; 0.000000,A (alanine),true,-1; 0.000000,S (serine),true,-1; 0.000000,P (proline),true,-1; 0.000000,V (valine),true,-1; 0.000000,T (threonine),true,-1; 0.000000,C (cysteine),false,-1; 0.000000,L (leucine),true,-1; 0.000000,I (isoleucine),true,-1; 0.000000,N (asparagine),true,-1; 0.000000,D (aspartic acid),true,-1; 0.000000,Q (glutamine),true,-1; 0.000000,K (lysine),true,-1; 0.000000,E (glutamic acid),true,-1; 0.000000,M (methionine),true,-1; 0.000000,H (histidine),true,-1; 0.000000,F (phenylalanine),true,-1; 0.000000,R (arginine),true,-1; 0.000000,Y (tyrosine),true,-1; 0.000000,W (tryptophan),true,-1; 0.000000,B ,true,-1; 0.000000,J,true,-1; 0.000000,O,true,-1; 0.000000,U,true,-1; 0.000000,X,true,-1; 0.000000,Z,true,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,false,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 57.021460,Cys Carbamidomethylation,true,2; 0.000000,site_07,false,1; 0.000000,site_08,false,1; 0.000000,site_09,false,1; 0.000000,site_10,false,1; 0.000000,site_11,false,1; 0.000000,site_12,false,1; 0.000000,site_13,false,1; 0.000000,site_14,false,1; 0.000000,site_15,false,1; 0.000000,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=100
msfragger.write_calibrated_mgf=true
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
path.textfield.msconvert=C\:\\Users\\jossmith\\AppData\\Local\\Apps\\ProteoWizard 3.0.20034.d7e41e31f 64-bit\\msconvert.exe
peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.run-percolator=false
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --mapmods --prot 0.01
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=false
phi-report.print-decoys=true
phi-report.prot-level-summary=true
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.assign_glycans=false
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=CHKYMSTW
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=5
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=1
ptmshepherd.precursor_tol=10
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=
ptmshepherd.prob_dhexY=
ptmshepherd.prob_neuacOx=
ptmshepherd.prob_neugcOx=
ptmshepherd.prob_phosphoOx=
ptmshepherd.prob_regY=
ptmshepherd.prob_sulfoOx=
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=false
ptmshepherd.run-shepherd=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=10
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=false
run-diaumpire=true
run-psm-validation=true
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0.1
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=true
speclibgen.use-easypqp=true
speclibgen.use-spectrast=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.freequant=--ptw 0.4 --tol 10 --isolated
tmtintegrator.groupby=0
tmtintegrator.labelquant=--tol 20 --level 2
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=C\:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=25
workflow.threads=7

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CheckCentroid
java -Xmx25G -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" com.dmtavt.fragpipe.util.CheckCentroid C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.mzXML 7
Done in 2104 ms.
Process 'CheckCentroid' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
INFO[15:34:54] Executing Workspace  v4.1.0                  
INFO[15:34:54] Removing workspace                           
WARN[15:34:54] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. 
INFO[15:34:54] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
WorkspaceCleanInit [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --init --nocheck
INFO[15:34:54] Executing Workspace  v4.1.0                  
INFO[15:34:54] Creating workspace                           
INFO[15:34:54] Done                                         
Process 'WorkspaceCleanInit' finished, exit code: 0
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
=================================================================================================
DIA-Umpire singal extraction analysis  (version: v2.2.3)
(c) University of Michigan
2021-11-17 15:34:54,677 INFO  [root] Version: v2.2.3
2021-11-17 15:34:54,678 INFO  [root] Parameter file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
2021-11-17 15:34:54,678 INFO  [root] Spectra file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.mzXML
2021-11-17 15:34:54,679 INFO  [root] 
2021-11-17 15:34:54,680 INFO  [root] ####################################################################################################
2021-11-17 15:34:54,680 INFO  [root] #No of threads
2021-11-17 15:34:54,680 INFO  [root] Thread = 7
2021-11-17 15:34:54,680 INFO  [root] ####################################################################################################
2021-11-17 15:34:54,680 INFO  [root] 
2021-11-17 15:34:54,680 INFO  [root] ## omit Thread
2021-11-17 15:34:54,680 INFO  [root] 
2021-11-17 15:34:54,680 INFO  [root] #Precursor-fragments grouping parameters
2021-11-17 15:34:54,680 INFO  [root] RPmax = 25
2021-11-17 15:34:54,680 INFO  [root] RFmax = 500
2021-11-17 15:34:54,680 INFO  [root] CorrThreshold = 0
2021-11-17 15:34:54,681 INFO  [root] DeltaApex = 0.2
2021-11-17 15:34:54,681 INFO  [root] RTOverlap = 0.3
2021-11-17 15:34:54,681 INFO  [root] 
2021-11-17 15:34:54,681 INFO  [root] #Fragment intensity adjustments
2021-11-17 15:34:54,681 INFO  [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2021-11-17 15:34:54,681 INFO  [root] AdjustFragIntensity = true
2021-11-17 15:34:54,682 INFO  [root] BoostComplementaryIon = false
2021-11-17 15:34:54,682 INFO  [root] 
2021-11-17 15:34:54,682 INFO  [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2021-11-17 15:34:54,682 INFO  [root] ExportPrecursorPeak = false
2021-11-17 15:34:54,682 INFO  [root] 
2021-11-17 15:34:54,682 INFO  [root] Q1 = true
2021-11-17 15:34:54,682 INFO  [root] Q2 = true
2021-11-17 15:34:54,682 INFO  [root] Q3 = true
2021-11-17 15:34:54,682 INFO  [root] 
2021-11-17 15:34:54,682 INFO  [root] #Signal extraction: mass accuracy and resolution
2021-11-17 15:34:54,682 INFO  [root] # resolution parameter matters only for data generated in profile mode
2021-11-17 15:34:54,682 INFO  [root] SE.MS1PPM = 10
2021-11-17 15:34:54,682 INFO  [root] SE.MS2PPM = 10
2021-11-17 15:34:54,683 INFO  [root] SE.Resolution = 60000
2021-11-17 15:34:54,683 INFO  [root] 
2021-11-17 15:34:54,683 INFO  [root] #Signal extraction: signal to noise filter
2021-11-17 15:34:54,683 INFO  [root] SE.SN = 1.1
2021-11-17 15:34:54,683 INFO  [root] SE.MS2SN = 1.1
2021-11-17 15:34:54,683 INFO  [root] 
2021-11-17 15:34:54,683 INFO  [root] #Signal extraction: minimum signal intensity filter
2021-11-17 15:34:54,683 INFO  [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2021-11-17 15:34:54,683 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2021-11-17 15:34:54,683 INFO  [root] SE.EstimateBG = false
2021-11-17 15:34:54,683 INFO  [root] SE.MinMSIntensity = 1
2021-11-17 15:34:54,683 INFO  [root] SE.MinMSMSIntensity = 1
2021-11-17 15:34:54,684 INFO  [root] 
2021-11-17 15:34:54,684 INFO  [root] #Signal extraction: peak curve detection and isotope grouping
2021-11-17 15:34:54,684 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2021-11-17 15:34:54,684 INFO  [root] SE.NoMissedScan = 1
2021-11-17 15:34:54,684 INFO  [root] SE.MaxCurveRTRange = 2
2021-11-17 15:34:54,684 INFO  [root] SE.RemoveGroupedPeaks = true
2021-11-17 15:34:54,684 INFO  [root] SE.RemoveGroupedPeaksRTOverlap = 0.3
2021-11-17 15:34:54,684 INFO  [root] SE.RemoveGroupedPeaksCorr = 0.3
2021-11-17 15:34:54,684 INFO  [root] SE.MinNoPeakCluster = 2
2021-11-17 15:34:54,684 INFO  [root] SE.MaxNoPeakCluster = 4
2021-11-17 15:34:54,861 INFO  [root] 
2021-11-17 15:34:54,861 INFO  [root] #Signal extraction: filtering of MS1 features
2021-11-17 15:34:54,862 INFO  [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2021-11-17 15:34:54,862 INFO  [root] SE.IsoPattern = 0.3
2021-11-17 15:34:54,862 INFO  [root] SE.MassDefectFilter = false
2021-11-17 15:34:54,862 INFO  [root] SE.MassDefectOffset = 0.1
2021-11-17 15:34:54,862 INFO  [root] 
2021-11-17 15:34:54,862 INFO  [root] #Signal extraction: other
2021-11-17 15:34:54,863 INFO  [root] SE.StartCharge = 1
2021-11-17 15:34:54,863 INFO  [root] SE.EndCharge = 5
2021-11-17 15:34:54,863 INFO  [root] SE.MS2StartCharge = 2
2021-11-17 15:34:54,863 INFO  [root] SE.MS2EndCharge = 5
2021-11-17 15:34:54,863 INFO  [root] SE.MinFrag = 10
2021-11-17 15:34:54,863 INFO  [root] SE.StartRT = 0
2021-11-17 15:34:54,863 INFO  [root] SE.EndRT = 9999
2021-11-17 15:34:54,863 INFO  [root] SE.MinMZ = 200
2021-11-17 15:34:54,863 INFO  [root] SE.MinPrecursorMass = 600
2021-11-17 15:34:54,863 INFO  [root] SE.MaxPrecursorMass = 5000
2021-11-17 15:34:54,863 INFO  [root] 
2021-11-17 15:34:54,864 INFO  [root] 
2021-11-17 15:34:54,864 INFO  [root] #Isolation window setting
2021-11-17 15:34:54,864 INFO  [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2021-11-17 15:34:54,864 INFO  [root] WindowType = SWATH
2021-11-17 15:34:54,864 INFO  [root] 
2021-11-17 15:34:54,864 INFO  [root] #Fix window size (For SWATH)
2021-11-17 15:34:54,864 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:34:54,864 INFO  [root] WindowSize = 10
2021-11-17 15:34:54,864 INFO  [root] 
2021-11-17 15:34:54,864 INFO  [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2021-11-17 15:34:54,864 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:34:54,864 INFO  [root] ==window setting begin
2021-11-17 15:34:54,864 INFO  [root] 
2021-11-17 15:34:54,864 INFO  [root] =================================================================================================
2021-11-17 15:34:54,864 INFO  [root] Processing C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.mzXML....
2021-11-17 15:34:54,875 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_diasetting.ser...
2021-11-17 15:34:54,886 INFO  [root] Writing parameter to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_params.ser...
2021-11-17 15:34:54,889 INFO  [root] Module A: Signal extraction
2021-11-17 15:34:57,411 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_diasetting.ser...
2021-11-17 15:34:57,898 INFO  [root] Processing MS1 peak detection
2021-11-17 15:34:57,899 INFO  [root] MS1 average cycle time : 2.6864002 seconds
2021-11-17 15:35:01,177 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:01,177 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:04,017 INFO  [root] 277503 Peak curves found (Memory usage:209MB)
2021-11-17 15:35:04,017 INFO  [root] Inclusion mz values found: 0/0
2021-11-17 15:35:04,017 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:04,019 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:10,970 INFO  [root] No of ion clusters:19302 (Memory usage:165MB)
2021-11-17 15:35:10,983 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_PeakCluster.serFS...
2021-11-17 15:35:11,218 INFO  [root] ==================================================================================
2021-11-17 15:35:11,218 INFO  [root] Processing DIA MS2 (mz range):977.0_980.0( 1/61 )
2021-11-17 15:35:11,300 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:11,300 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:11,947 INFO  [root] 29451 Peak curves found (Memory usage:191MB)
2021-11-17 15:35:11,957 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:11,957 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:12,229 INFO  [root] No of ion clusters:11 (Memory usage:193MB)
2021-11-17 15:35:12,229 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_977_980_PeakCluster.serFS...
2021-11-17 15:35:12,230 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:12,500 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:12,903 INFO  [root] ==================================================================================
2021-11-17 15:35:12,905 INFO  [root] Processing DIA MS2 (mz range):974.0_977.0( 2/61 )
2021-11-17 15:35:12,967 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:12,967 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:13,753 INFO  [root] 38665 Peak curves found (Memory usage:184MB)
2021-11-17 15:35:13,755 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:13,755 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:14,049 INFO  [root] No of ion clusters:5 (Memory usage:187MB)
2021-11-17 15:35:14,049 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_974_977_PeakCluster.serFS...
2021-11-17 15:35:14,051 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:14,326 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:14,566 INFO  [root] ==================================================================================
2021-11-17 15:35:14,566 INFO  [root] Processing DIA MS2 (mz range):971.0_974.0( 3/61 )
2021-11-17 15:35:14,618 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:14,619 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:15,254 INFO  [root] 59621 Peak curves found (Memory usage:192MB)
2021-11-17 15:35:15,257 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:15,257 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:15,536 INFO  [root] No of ion clusters:3 (Memory usage:197MB)
2021-11-17 15:35:15,536 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_971_974_PeakCluster.serFS...
2021-11-17 15:35:15,537 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:15,624 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:15,880 INFO  [root] ==================================================================================
2021-11-17 15:35:15,880 INFO  [root] Processing DIA MS2 (mz range):968.0_971.0( 4/61 )
2021-11-17 15:35:15,917 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:15,917 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:16,292 INFO  [root] 48990 Peak curves found (Memory usage:187MB)
2021-11-17 15:35:16,296 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:16,296 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:16,568 INFO  [root] No of ion clusters:8 (Memory usage:191MB)
2021-11-17 15:35:16,568 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_968_971_PeakCluster.serFS...
2021-11-17 15:35:16,569 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:16,636 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:16,864 INFO  [root] ==================================================================================
2021-11-17 15:35:16,864 INFO  [root] Processing DIA MS2 (mz range):965.0_968.0( 5/61 )
2021-11-17 15:35:16,889 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:16,889 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:17,127 INFO  [root] 48123 Peak curves found (Memory usage:187MB)
2021-11-17 15:35:17,128 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:17,129 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:17,387 INFO  [root] No of ion clusters:3 (Memory usage:191MB)
2021-11-17 15:35:17,387 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_965_968_PeakCluster.serFS...
2021-11-17 15:35:17,388 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:17,452 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:17,698 INFO  [root] ==================================================================================
2021-11-17 15:35:17,698 INFO  [root] Processing DIA MS2 (mz range):962.0_965.0( 6/61 )
2021-11-17 15:35:17,726 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:17,726 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:18,188 INFO  [root] 60455 Peak curves found (Memory usage:193MB)
2021-11-17 15:35:18,190 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:18,190 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:18,493 INFO  [root] No of ion clusters:12 (Memory usage:198MB)
2021-11-17 15:35:18,493 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_962_965_PeakCluster.serFS...
2021-11-17 15:35:18,494 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:18,594 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:18,804 INFO  [root] ==================================================================================
2021-11-17 15:35:18,804 INFO  [root] Processing DIA MS2 (mz range):959.0_962.0( 7/61 )
2021-11-17 15:35:18,837 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:18,837 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:19,388 INFO  [root] 60600 Peak curves found (Memory usage:194MB)
2021-11-17 15:35:19,390 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:19,390 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:19,697 INFO  [root] No of ion clusters:7 (Memory usage:198MB)
2021-11-17 15:35:19,697 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_959_962_PeakCluster.serFS...
2021-11-17 15:35:19,698 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:19,796 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:20,010 INFO  [root] ==================================================================================
2021-11-17 15:35:20,010 INFO  [root] Processing DIA MS2 (mz range):956.0_959.0( 8/61 )
2021-11-17 15:35:20,037 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:20,037 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:20,361 INFO  [root] 65569 Peak curves found (Memory usage:195MB)
2021-11-17 15:35:20,363 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:20,363 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:20,655 INFO  [root] No of ion clusters:3 (Memory usage:200MB)
2021-11-17 15:35:20,655 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_956_959_PeakCluster.serFS...
2021-11-17 15:35:20,656 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:20,730 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:20,950 INFO  [root] ==================================================================================
2021-11-17 15:35:20,950 INFO  [root] Processing DIA MS2 (mz range):953.0_956.0( 9/61 )
2021-11-17 15:35:20,984 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:20,984 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:21,955 INFO  [root] 64396 Peak curves found (Memory usage:197MB)
2021-11-17 15:35:21,957 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:21,957 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:22,257 INFO  [root] No of ion clusters:18 (Memory usage:202MB)
2021-11-17 15:35:22,257 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_953_956_PeakCluster.serFS...
2021-11-17 15:35:22,258 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:22,355 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:22,568 INFO  [root] ==================================================================================
2021-11-17 15:35:22,568 INFO  [root] Processing DIA MS2 (mz range):950.0_953.0( 10/61 )
2021-11-17 15:35:22,596 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:22,596 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:23,123 INFO  [root] 72236 Peak curves found (Memory usage:199MB)
2021-11-17 15:35:23,125 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:23,125 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:23,452 INFO  [root] No of ion clusters:10 (Memory usage:205MB)
2021-11-17 15:35:23,453 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_950_953_PeakCluster.serFS...
2021-11-17 15:35:23,453 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:23,529 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:23,750 INFO  [root] ==================================================================================
2021-11-17 15:35:23,750 INFO  [root] Processing DIA MS2 (mz range):947.0_950.0( 11/61 )
2021-11-17 15:35:23,785 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:23,785 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:24,340 INFO  [root] 70288 Peak curves found (Memory usage:199MB)
2021-11-17 15:35:24,342 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:24,342 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:24,660 INFO  [root] No of ion clusters:10 (Memory usage:204MB)
2021-11-17 15:35:24,660 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_947_950_PeakCluster.serFS...
2021-11-17 15:35:24,661 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:24,848 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:25,087 INFO  [root] ==================================================================================
2021-11-17 15:35:25,087 INFO  [root] Processing DIA MS2 (mz range):944.0_947.0( 12/61 )
2021-11-17 15:35:25,121 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:25,121 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:25,508 INFO  [root] 68678 Peak curves found (Memory usage:199MB)
2021-11-17 15:35:25,510 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:25,510 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:25,959 INFO  [root] No of ion clusters:15 (Memory usage:204MB)
2021-11-17 15:35:25,960 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_944_947_PeakCluster.serFS...
2021-11-17 15:35:25,960 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:26,046 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:26,265 INFO  [root] ==================================================================================
2021-11-17 15:35:26,265 INFO  [root] Processing DIA MS2 (mz range):941.0_944.0( 13/61 )
2021-11-17 15:35:26,293 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:26,294 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:26,760 INFO  [root] 66234 Peak curves found (Memory usage:199MB)
2021-11-17 15:35:26,763 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:26,763 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:27,058 INFO  [root] No of ion clusters:7 (Memory usage:204MB)
2021-11-17 15:35:27,058 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_941_944_PeakCluster.serFS...
2021-11-17 15:35:27,059 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:27,149 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:27,359 INFO  [root] ==================================================================================
2021-11-17 15:35:27,359 INFO  [root] Processing DIA MS2 (mz range):938.0_941.0( 14/61 )
2021-11-17 15:35:27,389 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:27,390 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:28,084 INFO  [root] 88166 Peak curves found (Memory usage:208MB)
2021-11-17 15:35:28,086 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:28,086 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:28,413 INFO  [root] No of ion clusters:12 (Memory usage:215MB)
2021-11-17 15:35:28,413 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_938_941_PeakCluster.serFS...
2021-11-17 15:35:28,414 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:28,518 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:28,733 INFO  [root] ==================================================================================
2021-11-17 15:35:28,733 INFO  [root] Processing DIA MS2 (mz range):935.0_938.0( 15/61 )
2021-11-17 15:35:28,762 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:28,763 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:29,791 INFO  [root] 78735 Peak curves found (Memory usage:206MB)
2021-11-17 15:35:29,793 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:29,793 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:30,104 INFO  [root] No of ion clusters:5 (Memory usage:212MB)
2021-11-17 15:35:30,104 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_935_938_PeakCluster.serFS...
2021-11-17 15:35:30,105 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:30,220 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:30,431 INFO  [root] ==================================================================================
2021-11-17 15:35:30,431 INFO  [root] Processing DIA MS2 (mz range):932.0_935.0( 16/61 )
2021-11-17 15:35:30,457 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:30,457 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:30,779 INFO  [root] 59056 Peak curves found (Memory usage:197MB)
2021-11-17 15:35:30,781 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:30,781 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:31,138 INFO  [root] No of ion clusters:12 (Memory usage:202MB)
2021-11-17 15:35:31,138 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_932_935_PeakCluster.serFS...
2021-11-17 15:35:31,139 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:31,223 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:31,438 INFO  [root] ==================================================================================
2021-11-17 15:35:31,438 INFO  [root] Processing DIA MS2 (mz range):929.0_932.0( 17/61 )
2021-11-17 15:35:31,463 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:31,463 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:31,739 INFO  [root] 56319 Peak curves found (Memory usage:197MB)
2021-11-17 15:35:31,742 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:31,742 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:32,019 INFO  [root] No of ion clusters:6 (Memory usage:201MB)
2021-11-17 15:35:32,019 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_929_932_PeakCluster.serFS...
2021-11-17 15:35:32,020 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:32,081 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:32,305 INFO  [root] ==================================================================================
2021-11-17 15:35:32,305 INFO  [root] Processing DIA MS2 (mz range):926.0_929.0( 18/61 )
2021-11-17 15:35:32,332 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:32,332 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:32,652 INFO  [root] 60170 Peak curves found (Memory usage:199MB)
2021-11-17 15:35:32,653 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:32,653 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:32,940 INFO  [root] No of ion clusters:7 (Memory usage:203MB)
2021-11-17 15:35:32,940 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_926_929_PeakCluster.serFS...
2021-11-17 15:35:32,941 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:33,018 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:33,235 INFO  [root] ==================================================================================
2021-11-17 15:35:33,235 INFO  [root] Processing DIA MS2 (mz range):923.0_926.0( 19/61 )
2021-11-17 15:35:33,257 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:33,257 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:33,556 INFO  [root] 55288 Peak curves found (Memory usage:198MB)
2021-11-17 15:35:33,557 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:33,557 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:33,838 INFO  [root] No of ion clusters:4 (Memory usage:202MB)
2021-11-17 15:35:33,838 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_923_926_PeakCluster.serFS...
2021-11-17 15:35:33,838 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:33,924 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:34,138 INFO  [root] ==================================================================================
2021-11-17 15:35:34,139 INFO  [root] Processing DIA MS2 (mz range):920.0_923.0( 20/61 )
2021-11-17 15:35:34,167 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:34,167 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:34,477 INFO  [root] 64048 Peak curves found (Memory usage:201MB)
2021-11-17 15:35:34,479 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:34,479 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:34,789 INFO  [root] No of ion clusters:7 (Memory usage:206MB)
2021-11-17 15:35:34,789 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_920_923_PeakCluster.serFS...
2021-11-17 15:35:34,791 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:34,866 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:35,085 INFO  [root] ==================================================================================
2021-11-17 15:35:35,085 INFO  [root] Processing DIA MS2 (mz range):917.0_920.0( 21/61 )
2021-11-17 15:35:35,111 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:35,111 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:35,745 INFO  [root] 61267 Peak curves found (Memory usage:201MB)
2021-11-17 15:35:35,748 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:35,748 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:36,040 INFO  [root] No of ion clusters:3 (Memory usage:206MB)
2021-11-17 15:35:36,040 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_917_920_PeakCluster.serFS...
2021-11-17 15:35:36,041 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:36,136 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:36,339 INFO  [root] ==================================================================================
2021-11-17 15:35:36,339 INFO  [root] Processing DIA MS2 (mz range):914.0_917.0( 22/61 )
2021-11-17 15:35:36,361 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:36,361 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:36,702 INFO  [root] 63094 Peak curves found (Memory usage:201MB)
2021-11-17 15:35:36,705 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:36,705 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:36,996 INFO  [root] No of ion clusters:6 (Memory usage:206MB)
2021-11-17 15:35:36,997 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_914_917_PeakCluster.serFS...
2021-11-17 15:35:36,997 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:37,058 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:37,272 INFO  [root] ==================================================================================
2021-11-17 15:35:37,272 INFO  [root] Processing DIA MS2 (mz range):911.0_914.0( 23/61 )
2021-11-17 15:35:37,294 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:37,294 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:37,644 INFO  [root] 56162 Peak curves found (Memory usage:199MB)
2021-11-17 15:35:37,646 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:37,646 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:37,928 INFO  [root] No of ion clusters:6 (Memory usage:203MB)
2021-11-17 15:35:37,928 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_911_914_PeakCluster.serFS...
2021-11-17 15:35:37,929 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:38,021 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:38,265 INFO  [root] ==================================================================================
2021-11-17 15:35:38,265 INFO  [root] Processing DIA MS2 (mz range):908.0_911.0( 24/61 )
2021-11-17 15:35:38,289 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:38,289 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:38,583 INFO  [root] 56586 Peak curves found (Memory usage:199MB)
2021-11-17 15:35:38,585 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:38,585 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:38,885 INFO  [root] No of ion clusters:5 (Memory usage:204MB)
2021-11-17 15:35:38,885 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_908_911_PeakCluster.serFS...
2021-11-17 15:35:38,887 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:38,966 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:39,205 INFO  [root] ==================================================================================
2021-11-17 15:35:39,205 INFO  [root] Processing DIA MS2 (mz range):905.0_908.0( 25/61 )
2021-11-17 15:35:39,227 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:39,227 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:39,533 INFO  [root] 58037 Peak curves found (Memory usage:200MB)
2021-11-17 15:35:39,537 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:39,537 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:39,851 INFO  [root] No of ion clusters:7 (Memory usage:205MB)
2021-11-17 15:35:39,851 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_905_908_PeakCluster.serFS...
2021-11-17 15:35:39,852 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:39,909 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:40,146 INFO  [root] ==================================================================================
2021-11-17 15:35:40,146 INFO  [root] Processing DIA MS2 (mz range):902.0_905.0( 26/61 )
2021-11-17 15:35:40,173 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:40,173 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:40,448 INFO  [root] 55432 Peak curves found (Memory usage:200MB)
2021-11-17 15:35:40,450 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:40,450 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:40,725 INFO  [root] No of ion clusters:11 (Memory usage:204MB)
2021-11-17 15:35:40,726 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_902_905_PeakCluster.serFS...
2021-11-17 15:35:40,726 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:40,782 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:41,004 INFO  [root] ==================================================================================
2021-11-17 15:35:41,004 INFO  [root] Processing DIA MS2 (mz range):899.0_902.0( 27/61 )
2021-11-17 15:35:41,030 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:41,030 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:41,372 INFO  [root] 58643 Peak curves found (Memory usage:201MB)
2021-11-17 15:35:41,374 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:41,374 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:41,656 INFO  [root] No of ion clusters:4 (Memory usage:206MB)
2021-11-17 15:35:41,656 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_899_902_PeakCluster.serFS...
2021-11-17 15:35:41,657 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:41,714 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:41,937 INFO  [root] ==================================================================================
2021-11-17 15:35:41,937 INFO  [root] Processing DIA MS2 (mz range):896.0_899.0( 28/61 )
2021-11-17 15:35:41,963 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:41,963 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:42,266 INFO  [root] 65477 Peak curves found (Memory usage:205MB)
2021-11-17 15:35:42,268 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:42,268 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:42,562 INFO  [root] No of ion clusters:9 (Memory usage:210MB)
2021-11-17 15:35:42,562 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_896_899_PeakCluster.serFS...
2021-11-17 15:35:42,563 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:42,662 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:42,903 INFO  [root] ==================================================================================
2021-11-17 15:35:42,903 INFO  [root] Processing DIA MS2 (mz range):893.0_896.0( 29/61 )
2021-11-17 15:35:42,929 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:42,929 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:43,274 INFO  [root] 67179 Peak curves found (Memory usage:206MB)
2021-11-17 15:35:43,276 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:43,276 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:43,621 INFO  [root] No of ion clusters:1 (Memory usage:211MB)
2021-11-17 15:35:43,621 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_893_896_PeakCluster.serFS...
2021-11-17 15:35:43,622 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:43,722 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:43,932 INFO  [root] ==================================================================================
2021-11-17 15:35:43,932 INFO  [root] Processing DIA MS2 (mz range):890.0_893.0( 30/61 )
2021-11-17 15:35:43,961 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:43,961 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:44,261 INFO  [root] 62875 Peak curves found (Memory usage:204MB)
2021-11-17 15:35:44,263 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:44,263 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:44,556 INFO  [root] No of ion clusters:4 (Memory usage:209MB)
2021-11-17 15:35:44,556 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_890_893_PeakCluster.serFS...
2021-11-17 15:35:44,557 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:44,637 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:44,869 INFO  [root] ==================================================================================
2021-11-17 15:35:44,869 INFO  [root] Processing DIA MS2 (mz range):887.0_890.0( 31/61 )
2021-11-17 15:35:44,896 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:44,896 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:45,336 INFO  [root] 53772 Peak curves found (Memory usage:201MB)
2021-11-17 15:35:45,338 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:45,338 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:45,632 INFO  [root] No of ion clusters:6 (Memory usage:205MB)
2021-11-17 15:35:45,632 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_887_890_PeakCluster.serFS...
2021-11-17 15:35:45,632 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:45,701 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:45,941 INFO  [root] ==================================================================================
2021-11-17 15:35:45,941 INFO  [root] Processing DIA MS2 (mz range):884.0_887.0( 32/61 )
2021-11-17 15:35:45,965 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:45,965 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:46,365 INFO  [root] 49076 Peak curves found (Memory usage:200MB)
2021-11-17 15:35:46,366 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:46,366 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:46,652 INFO  [root] No of ion clusters:3 (Memory usage:204MB)
2021-11-17 15:35:46,652 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_884_887_PeakCluster.serFS...
2021-11-17 15:35:46,653 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:46,714 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:46,934 INFO  [root] ==================================================================================
2021-11-17 15:35:46,934 INFO  [root] Processing DIA MS2 (mz range):881.0_884.0( 33/61 )
2021-11-17 15:35:46,963 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:46,963 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:47,229 INFO  [root] 46646 Peak curves found (Memory usage:199MB)
2021-11-17 15:35:47,231 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:47,231 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:47,494 INFO  [root] No of ion clusters:4 (Memory usage:203MB)
2021-11-17 15:35:47,494 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_881_884_PeakCluster.serFS...
2021-11-17 15:35:47,495 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:47,555 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:47,776 INFO  [root] ==================================================================================
2021-11-17 15:35:47,776 INFO  [root] Processing DIA MS2 (mz range):878.0_881.0( 34/61 )
2021-11-17 15:35:47,798 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:47,798 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:48,086 INFO  [root] 47383 Peak curves found (Memory usage:200MB)
2021-11-17 15:35:48,089 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:48,089 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:48,384 INFO  [root] No of ion clusters:5 (Memory usage:203MB)
2021-11-17 15:35:48,385 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_878_881_PeakCluster.serFS...
2021-11-17 15:35:48,385 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:48,461 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:48,759 INFO  [root] ==================================================================================
2021-11-17 15:35:48,759 INFO  [root] Processing DIA MS2 (mz range):875.0_878.0( 35/61 )
2021-11-17 15:35:48,789 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:48,789 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:49,060 INFO  [root] 55453 Peak curves found (Memory usage:203MB)
2021-11-17 15:35:49,062 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:49,062 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:49,340 INFO  [root] No of ion clusters:3 (Memory usage:207MB)
2021-11-17 15:35:49,340 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_875_878_PeakCluster.serFS...
2021-11-17 15:35:49,340 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:49,412 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:49,650 INFO  [root] ==================================================================================
2021-11-17 15:35:49,650 INFO  [root] Processing DIA MS2 (mz range):872.0_875.0( 36/61 )
2021-11-17 15:35:49,677 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:49,677 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:50,263 INFO  [root] 62524 Peak curves found (Memory usage:207MB)
2021-11-17 15:35:50,265 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:50,265 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:50,552 INFO  [root] No of ion clusters:5 (Memory usage:212MB)
2021-11-17 15:35:50,552 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_872_875_PeakCluster.serFS...
2021-11-17 15:35:50,554 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:50,654 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:50,867 INFO  [root] ==================================================================================
2021-11-17 15:35:50,867 INFO  [root] Processing DIA MS2 (mz range):869.0_872.0( 37/61 )
2021-11-17 15:35:50,889 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:50,889 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:51,276 INFO  [root] 62743 Peak curves found (Memory usage:207MB)
2021-11-17 15:35:51,279 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:51,279 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:51,587 INFO  [root] No of ion clusters:4 (Memory usage:211MB)
2021-11-17 15:35:51,587 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_869_872_PeakCluster.serFS...
2021-11-17 15:35:51,588 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:51,657 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:51,882 INFO  [root] ==================================================================================
2021-11-17 15:35:51,882 INFO  [root] Processing DIA MS2 (mz range):866.0_869.0( 38/61 )
2021-11-17 15:35:51,905 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:51,905 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:52,242 INFO  [root] 53423 Peak curves found (Memory usage:204MB)
2021-11-17 15:35:52,244 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:52,244 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:52,537 INFO  [root] No of ion clusters:4 (Memory usage:208MB)
2021-11-17 15:35:52,537 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_866_869_PeakCluster.serFS...
2021-11-17 15:35:52,538 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:52,609 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:52,818 INFO  [root] ==================================================================================
2021-11-17 15:35:52,819 INFO  [root] Processing DIA MS2 (mz range):863.0_866.0( 39/61 )
2021-11-17 15:35:52,842 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:52,842 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:53,133 INFO  [root] 54485 Peak curves found (Memory usage:205MB)
2021-11-17 15:35:53,135 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:53,135 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:53,401 INFO  [root] No of ion clusters:11 (Memory usage:209MB)
2021-11-17 15:35:53,401 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_863_866_PeakCluster.serFS...
2021-11-17 15:35:53,402 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:53,489 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:53,769 INFO  [root] ==================================================================================
2021-11-17 15:35:53,769 INFO  [root] Processing DIA MS2 (mz range):860.0_863.0( 40/61 )
2021-11-17 15:35:53,791 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:53,792 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:54,075 INFO  [root] 55335 Peak curves found (Memory usage:205MB)
2021-11-17 15:35:54,077 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:54,077 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:54,349 INFO  [root] No of ion clusters:6 (Memory usage:209MB)
2021-11-17 15:35:54,349 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_860_863_PeakCluster.serFS...
2021-11-17 15:35:54,350 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:54,442 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:54,667 INFO  [root] ==================================================================================
2021-11-17 15:35:54,667 INFO  [root] Processing DIA MS2 (mz range):857.0_860.0( 41/61 )
2021-11-17 15:35:54,691 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:54,691 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:54,999 INFO  [root] 57058 Peak curves found (Memory usage:206MB)
2021-11-17 15:35:55,000 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:55,000 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:55,291 INFO  [root] No of ion clusters:9 (Memory usage:210MB)
2021-11-17 15:35:55,291 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_857_860_PeakCluster.serFS...
2021-11-17 15:35:55,292 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:55,401 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:55,620 INFO  [root] ==================================================================================
2021-11-17 15:35:55,620 INFO  [root] Processing DIA MS2 (mz range):854.0_857.0( 42/61 )
2021-11-17 15:35:55,646 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:55,646 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:56,030 INFO  [root] 63188 Peak curves found (Memory usage:209MB)
2021-11-17 15:35:56,033 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:56,033 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:56,337 INFO  [root] No of ion clusters:6 (Memory usage:214MB)
2021-11-17 15:35:56,337 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_854_857_PeakCluster.serFS...
2021-11-17 15:35:56,338 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:56,441 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:56,686 INFO  [root] ==================================================================================
2021-11-17 15:35:56,686 INFO  [root] Processing DIA MS2 (mz range):851.0_854.0( 43/61 )
2021-11-17 15:35:56,714 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:56,714 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:57,079 INFO  [root] 69883 Peak curves found (Memory usage:212MB)
2021-11-17 15:35:57,081 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:57,081 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:57,384 INFO  [root] No of ion clusters:9 (Memory usage:217MB)
2021-11-17 15:35:57,384 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_851_854_PeakCluster.serFS...
2021-11-17 15:35:57,385 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:57,461 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:57,682 INFO  [root] ==================================================================================
2021-11-17 15:35:57,682 INFO  [root] Processing DIA MS2 (mz range):848.0_851.0( 44/61 )
2021-11-17 15:35:57,709 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:57,709 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:58,276 INFO  [root] 59699 Peak curves found (Memory usage:209MB)
2021-11-17 15:35:58,277 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:58,277 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:58,580 INFO  [root] No of ion clusters:6 (Memory usage:213MB)
2021-11-17 15:35:58,580 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_848_851_PeakCluster.serFS...
2021-11-17 15:35:58,581 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:58,689 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:58,908 INFO  [root] ==================================================================================
2021-11-17 15:35:58,908 INFO  [root] Processing DIA MS2 (mz range):845.0_848.0( 45/61 )
2021-11-17 15:35:58,932 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:58,932 INFO  [root] Smoothing detected signals......
2021-11-17 15:35:59,351 INFO  [root] 64758 Peak curves found (Memory usage:211MB)
2021-11-17 15:35:59,353 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:35:59,353 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:35:59,658 INFO  [root] No of ion clusters:3 (Memory usage:216MB)
2021-11-17 15:35:59,658 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_845_848_PeakCluster.serFS...
2021-11-17 15:35:59,659 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:35:59,747 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:35:59,960 INFO  [root] ==================================================================================
2021-11-17 15:35:59,960 INFO  [root] Processing DIA MS2 (mz range):842.0_845.0( 46/61 )
2021-11-17 15:35:59,986 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:35:59,986 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:00,377 INFO  [root] 55094 Peak curves found (Memory usage:206MB)
2021-11-17 15:36:00,379 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:00,379 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:00,691 INFO  [root] No of ion clusters:7 (Memory usage:210MB)
2021-11-17 15:36:00,691 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_842_845_PeakCluster.serFS...
2021-11-17 15:36:00,692 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:00,789 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:01,023 INFO  [root] ==================================================================================
2021-11-17 15:36:01,023 INFO  [root] Processing DIA MS2 (mz range):839.0_842.0( 47/61 )
2021-11-17 15:36:01,047 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:01,047 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:01,384 INFO  [root] 58532 Peak curves found (Memory usage:208MB)
2021-11-17 15:36:01,386 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:01,386 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:01,708 INFO  [root] No of ion clusters:4 (Memory usage:213MB)
2021-11-17 15:36:01,708 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_839_842_PeakCluster.serFS...
2021-11-17 15:36:01,708 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:01,817 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:02,033 INFO  [root] ==================================================================================
2021-11-17 15:36:02,033 INFO  [root] Processing DIA MS2 (mz range):836.0_839.0( 48/61 )
2021-11-17 15:36:02,061 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:02,061 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:02,510 INFO  [root] 61045 Peak curves found (Memory usage:209MB)
2021-11-17 15:36:02,511 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:02,511 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:02,856 INFO  [root] No of ion clusters:11 (Memory usage:214MB)
2021-11-17 15:36:02,856 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_836_839_PeakCluster.serFS...
2021-11-17 15:36:02,857 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:02,966 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:03,196 INFO  [root] ==================================================================================
2021-11-17 15:36:03,196 INFO  [root] Processing DIA MS2 (mz range):833.0_836.0( 49/61 )
2021-11-17 15:36:03,222 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:03,222 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:03,618 INFO  [root] 65244 Peak curves found (Memory usage:211MB)
2021-11-17 15:36:03,620 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:03,620 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:03,957 INFO  [root] No of ion clusters:6 (Memory usage:216MB)
2021-11-17 15:36:03,957 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_833_836_PeakCluster.serFS...
2021-11-17 15:36:03,958 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:04,060 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:04,309 INFO  [root] ==================================================================================
2021-11-17 15:36:04,309 INFO  [root] Processing DIA MS2 (mz range):830.0_833.0( 50/61 )
2021-11-17 15:36:04,333 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:04,333 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:04,726 INFO  [root] 65720 Peak curves found (Memory usage:212MB)
2021-11-17 15:36:04,728 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:04,728 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:05,040 INFO  [root] No of ion clusters:6 (Memory usage:217MB)
2021-11-17 15:36:05,040 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_830_833_PeakCluster.serFS...
2021-11-17 15:36:05,041 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:05,146 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:05,369 INFO  [root] ==================================================================================
2021-11-17 15:36:05,369 INFO  [root] Processing DIA MS2 (mz range):827.0_830.0( 51/61 )
2021-11-17 15:36:05,395 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:05,395 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:05,803 INFO  [root] 65268 Peak curves found (Memory usage:212MB)
2021-11-17 15:36:05,805 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:05,805 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:06,116 INFO  [root] No of ion clusters:5 (Memory usage:217MB)
2021-11-17 15:36:06,116 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_827_830_PeakCluster.serFS...
2021-11-17 15:36:06,117 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:06,210 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:06,430 INFO  [root] ==================================================================================
2021-11-17 15:36:06,430 INFO  [root] Processing DIA MS2 (mz range):824.0_827.0( 52/61 )
2021-11-17 15:36:06,456 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:06,456 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:06,772 INFO  [root] 67707 Peak curves found (Memory usage:213MB)
2021-11-17 15:36:06,774 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:06,774 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:07,089 INFO  [root] No of ion clusters:5 (Memory usage:218MB)
2021-11-17 15:36:07,089 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_824_827_PeakCluster.serFS...
2021-11-17 15:36:07,090 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:07,180 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:07,401 INFO  [root] ==================================================================================
2021-11-17 15:36:07,401 INFO  [root] Processing DIA MS2 (mz range):821.0_824.0( 53/61 )
2021-11-17 15:36:07,429 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:07,429 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:07,786 INFO  [root] 74208 Peak curves found (Memory usage:216MB)
2021-11-17 15:36:07,788 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:07,788 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:08,104 INFO  [root] No of ion clusters:7 (Memory usage:222MB)
2021-11-17 15:36:08,104 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_821_824_PeakCluster.serFS...
2021-11-17 15:36:08,105 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:08,220 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:08,456 INFO  [root] ==================================================================================
2021-11-17 15:36:08,456 INFO  [root] Processing DIA MS2 (mz range):818.0_821.0( 54/61 )
2021-11-17 15:36:08,489 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:08,489 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:08,991 INFO  [root] 84032 Peak curves found (Memory usage:221MB)
2021-11-17 15:36:08,993 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:08,993 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:09,324 INFO  [root] No of ion clusters:8 (Memory usage:227MB)
2021-11-17 15:36:09,324 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_818_821_PeakCluster.serFS...
2021-11-17 15:36:09,325 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:09,502 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:09,769 INFO  [root] ==================================================================================
2021-11-17 15:36:09,769 INFO  [root] Processing DIA MS2 (mz range):815.0_818.0( 55/61 )
2021-11-17 15:36:09,798 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:09,798 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:10,315 INFO  [root] 77624 Peak curves found (Memory usage:219MB)
2021-11-17 15:36:10,317 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:10,317 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:10,647 INFO  [root] No of ion clusters:5 (Memory usage:224MB)
2021-11-17 15:36:10,647 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_815_818_PeakCluster.serFS...
2021-11-17 15:36:10,648 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:10,778 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:11,030 INFO  [root] ==================================================================================
2021-11-17 15:36:11,030 INFO  [root] Processing DIA MS2 (mz range):812.0_815.0( 56/61 )
2021-11-17 15:36:11,056 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:11,057 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:11,500 INFO  [root] 68661 Peak curves found (Memory usage:215MB)
2021-11-17 15:36:11,501 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:11,501 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:11,822 INFO  [root] No of ion clusters:6 (Memory usage:220MB)
2021-11-17 15:36:11,822 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_812_815_PeakCluster.serFS...
2021-11-17 15:36:11,823 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:11,941 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:12,173 INFO  [root] ==================================================================================
2021-11-17 15:36:12,173 INFO  [root] Processing DIA MS2 (mz range):809.0_812.0( 57/61 )
2021-11-17 15:36:12,199 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:12,199 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:12,529 INFO  [root] 65629 Peak curves found (Memory usage:214MB)
2021-11-17 15:36:12,531 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:12,531 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:12,882 INFO  [root] No of ion clusters:10 (Memory usage:219MB)
2021-11-17 15:36:12,882 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_809_812_PeakCluster.serFS...
2021-11-17 15:36:12,883 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:12,989 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:13,228 INFO  [root] ==================================================================================
2021-11-17 15:36:13,228 INFO  [root] Processing DIA MS2 (mz range):806.0_809.0( 58/61 )
2021-11-17 15:36:13,253 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:13,253 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:13,582 INFO  [root] 65972 Peak curves found (Memory usage:214MB)
2021-11-17 15:36:13,584 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:13,584 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:13,889 INFO  [root] No of ion clusters:9 (Memory usage:219MB)
2021-11-17 15:36:13,889 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_806_809_PeakCluster.serFS...
2021-11-17 15:36:13,891 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:14,021 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:14,294 INFO  [root] ==================================================================================
2021-11-17 15:36:14,294 INFO  [root] Processing DIA MS2 (mz range):803.0_806.0( 59/61 )
2021-11-17 15:36:14,326 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:14,326 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:14,803 INFO  [root] 68956 Peak curves found (Memory usage:215MB)
2021-11-17 15:36:14,805 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:14,805 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:15,133 INFO  [root] No of ion clusters:5 (Memory usage:221MB)
2021-11-17 15:36:15,134 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_803_806_PeakCluster.serFS...
2021-11-17 15:36:15,134 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:15,275 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:15,546 INFO  [root] ==================================================================================
2021-11-17 15:36:15,546 INFO  [root] Processing DIA MS2 (mz range):800.0_803.0( 60/61 )
2021-11-17 15:36:15,577 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:15,577 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:15,890 INFO  [root] 41519 Peak curves found (Memory usage:205MB)
2021-11-17 15:36:15,892 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:15,892 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:16,185 INFO  [root] No of ion clusters:4 (Memory usage:208MB)
2021-11-17 15:36:16,185 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_800_803_PeakCluster.serFS...
2021-11-17 15:36:16,186 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:16,284 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:16,513 INFO  [root] ==================================================================================
2021-11-17 15:36:16,513 INFO  [root] Processing DIA MS2 (mz range):797.0_800.0( 61/61 )
2021-11-17 15:36:16,531 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:16,531 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:17,199 INFO  [root] 37472 Peak curves found (Memory usage:206MB)
2021-11-17 15:36:17,201 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:17,201 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:17,466 INFO  [root] No of ion clusters:29 (Memory usage:209MB)
2021-11-17 15:36:17,466 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_797_800_PeakCluster.serFS...
2021-11-17 15:36:17,467 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:17,724 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:18,048 INFO  [root] ==================================================================================
2021-11-17 15:36:18,782 INFO  [root] C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.mzXML processed time:0 hour, 1 min, 23 sec
2021-11-17 15:36:18,782 INFO  [root] Job complete
2021-11-17 15:36:18,782 INFO  [root] =================================================================================================
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
=================================================================================================
DIA-Umpire singal extraction analysis  (version: v2.2.3)
(c) University of Michigan
2021-11-17 15:36:25,866 INFO  [root] Version: v2.2.3
2021-11-17 15:36:25,866 INFO  [root] Parameter file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
2021-11-17 15:36:25,867 INFO  [root] Spectra file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.mzXML
2021-11-17 15:36:25,869 INFO  [root] 
2021-11-17 15:36:25,869 INFO  [root] ####################################################################################################
2021-11-17 15:36:25,869 INFO  [root] #No of threads
2021-11-17 15:36:25,869 INFO  [root] Thread = 7
2021-11-17 15:36:25,869 INFO  [root] ####################################################################################################
2021-11-17 15:36:25,869 INFO  [root] 
2021-11-17 15:36:25,869 INFO  [root] ## omit Thread
2021-11-17 15:36:25,869 INFO  [root] 
2021-11-17 15:36:25,869 INFO  [root] #Precursor-fragments grouping parameters
2021-11-17 15:36:25,869 INFO  [root] RPmax = 25
2021-11-17 15:36:25,870 INFO  [root] RFmax = 500
2021-11-17 15:36:25,870 INFO  [root] CorrThreshold = 0
2021-11-17 15:36:25,870 INFO  [root] DeltaApex = 0.2
2021-11-17 15:36:25,871 INFO  [root] RTOverlap = 0.3
2021-11-17 15:36:25,871 INFO  [root] 
2021-11-17 15:36:25,871 INFO  [root] #Fragment intensity adjustments
2021-11-17 15:36:25,871 INFO  [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2021-11-17 15:36:25,871 INFO  [root] AdjustFragIntensity = true
2021-11-17 15:36:25,871 INFO  [root] BoostComplementaryIon = false
2021-11-17 15:36:25,871 INFO  [root] 
2021-11-17 15:36:25,871 INFO  [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2021-11-17 15:36:25,871 INFO  [root] ExportPrecursorPeak = false
2021-11-17 15:36:25,872 INFO  [root] 
2021-11-17 15:36:25,872 INFO  [root] Q1 = true
2021-11-17 15:36:25,872 INFO  [root] Q2 = true
2021-11-17 15:36:25,872 INFO  [root] Q3 = true
2021-11-17 15:36:25,872 INFO  [root] 
2021-11-17 15:36:25,872 INFO  [root] #Signal extraction: mass accuracy and resolution
2021-11-17 15:36:25,872 INFO  [root] # resolution parameter matters only for data generated in profile mode
2021-11-17 15:36:25,872 INFO  [root] SE.MS1PPM = 10
2021-11-17 15:36:25,872 INFO  [root] SE.MS2PPM = 10
2021-11-17 15:36:25,872 INFO  [root] SE.Resolution = 60000
2021-11-17 15:36:25,872 INFO  [root] 
2021-11-17 15:36:25,872 INFO  [root] #Signal extraction: signal to noise filter
2021-11-17 15:36:25,872 INFO  [root] SE.SN = 1.1
2021-11-17 15:36:25,873 INFO  [root] SE.MS2SN = 1.1
2021-11-17 15:36:25,873 INFO  [root] 
2021-11-17 15:36:25,873 INFO  [root] #Signal extraction: minimum signal intensity filter
2021-11-17 15:36:25,873 INFO  [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2021-11-17 15:36:25,873 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2021-11-17 15:36:25,873 INFO  [root] SE.EstimateBG = false
2021-11-17 15:36:25,873 INFO  [root] SE.MinMSIntensity = 1
2021-11-17 15:36:25,874 INFO  [root] SE.MinMSMSIntensity = 1
2021-11-17 15:36:25,874 INFO  [root] 
2021-11-17 15:36:25,874 INFO  [root] #Signal extraction: peak curve detection and isotope grouping
2021-11-17 15:36:25,874 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2021-11-17 15:36:25,874 INFO  [root] SE.NoMissedScan = 1
2021-11-17 15:36:25,874 INFO  [root] SE.MaxCurveRTRange = 2
2021-11-17 15:36:25,874 INFO  [root] SE.RemoveGroupedPeaks = true
2021-11-17 15:36:25,874 INFO  [root] SE.RemoveGroupedPeaksRTOverlap = 0.3
2021-11-17 15:36:25,874 INFO  [root] SE.RemoveGroupedPeaksCorr = 0.3
2021-11-17 15:36:25,874 INFO  [root] SE.MinNoPeakCluster = 2
2021-11-17 15:36:25,874 INFO  [root] SE.MaxNoPeakCluster = 4
2021-11-17 15:36:25,874 INFO  [root] 
2021-11-17 15:36:25,874 INFO  [root] #Signal extraction: filtering of MS1 features
2021-11-17 15:36:25,875 INFO  [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2021-11-17 15:36:25,875 INFO  [root] SE.IsoPattern = 0.3
2021-11-17 15:36:26,073 INFO  [root] SE.MassDefectFilter = false
2021-11-17 15:36:26,073 INFO  [root] SE.MassDefectOffset = 0.1
2021-11-17 15:36:26,073 INFO  [root] 
2021-11-17 15:36:26,073 INFO  [root] #Signal extraction: other
2021-11-17 15:36:26,073 INFO  [root] SE.StartCharge = 1
2021-11-17 15:36:26,074 INFO  [root] SE.EndCharge = 5
2021-11-17 15:36:26,074 INFO  [root] SE.MS2StartCharge = 2
2021-11-17 15:36:26,074 INFO  [root] SE.MS2EndCharge = 5
2021-11-17 15:36:26,074 INFO  [root] SE.MinFrag = 10
2021-11-17 15:36:26,074 INFO  [root] SE.StartRT = 0
2021-11-17 15:36:26,074 INFO  [root] SE.EndRT = 9999
2021-11-17 15:36:26,074 INFO  [root] SE.MinMZ = 200
2021-11-17 15:36:26,074 INFO  [root] SE.MinPrecursorMass = 600
2021-11-17 15:36:26,074 INFO  [root] SE.MaxPrecursorMass = 5000
2021-11-17 15:36:26,074 INFO  [root] 
2021-11-17 15:36:26,074 INFO  [root] 
2021-11-17 15:36:26,074 INFO  [root] #Isolation window setting
2021-11-17 15:36:26,074 INFO  [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2021-11-17 15:36:26,074 INFO  [root] WindowType = SWATH
2021-11-17 15:36:26,074 INFO  [root] 
2021-11-17 15:36:26,074 INFO  [root] #Fix window size (For SWATH)
2021-11-17 15:36:26,074 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:36:26,074 INFO  [root] WindowSize = 10
2021-11-17 15:36:26,075 INFO  [root] 
2021-11-17 15:36:26,075 INFO  [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2021-11-17 15:36:26,075 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:36:26,075 INFO  [root] ==window setting begin
2021-11-17 15:36:26,075 INFO  [root] 
2021-11-17 15:36:26,075 INFO  [root] =================================================================================================
2021-11-17 15:36:26,075 INFO  [root] Processing C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.mzXML....
2021-11-17 15:36:26,079 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_diasetting.ser...
2021-11-17 15:36:26,087 INFO  [root] Writing parameter to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_params.ser...
2021-11-17 15:36:26,089 INFO  [root] Module A: Signal extraction
2021-11-17 15:36:30,642 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_diasetting.ser...
2021-11-17 15:36:31,123 INFO  [root] Processing MS1 peak detection
2021-11-17 15:36:31,124 INFO  [root] MS1 average cycle time : 2.6747808 seconds
2021-11-17 15:36:36,375 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:36,375 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:41,076 INFO  [root] 286635 Peak curves found (Memory usage:305MB)
2021-11-17 15:36:41,076 INFO  [root] Inclusion mz values found: 0/0
2021-11-17 15:36:41,076 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:41,077 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:48,998 INFO  [root] No of ion clusters:30383 (Memory usage:181MB)
2021-11-17 15:36:49,018 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_PeakCluster.serFS...
2021-11-17 15:36:49,295 INFO  [root] ==================================================================================
2021-11-17 15:36:49,295 INFO  [root] Processing DIA MS2 (mz range):977.0_980.0( 1/61 )
2021-11-17 15:36:49,383 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:49,384 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:50,435 INFO  [root] 69357 Peak curves found (Memory usage:228MB)
2021-11-17 15:36:50,439 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:50,439 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:50,760 INFO  [root] No of ion clusters:50 (Memory usage:234MB)
2021-11-17 15:36:50,760 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_977_980_PeakCluster.serFS...
2021-11-17 15:36:50,762 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:51,648 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:52,356 INFO  [root] ==================================================================================
2021-11-17 15:36:52,356 INFO  [root] Processing DIA MS2 (mz range):974.0_977.0( 2/61 )
2021-11-17 15:36:52,435 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:52,435 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:53,405 INFO  [root] 100233 Peak curves found (Memory usage:228MB)
2021-11-17 15:36:53,407 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:53,407 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:53,771 INFO  [root] No of ion clusters:18 (Memory usage:236MB)
2021-11-17 15:36:53,771 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_974_977_PeakCluster.serFS...
2021-11-17 15:36:53,772 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:54,037 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:54,366 INFO  [root] ==================================================================================
2021-11-17 15:36:54,366 INFO  [root] Processing DIA MS2 (mz range):971.0_974.0( 3/61 )
2021-11-17 15:36:54,438 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:54,438 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:55,778 INFO  [root] 147847 Peak curves found (Memory usage:249MB)
2021-11-17 15:36:55,781 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:55,781 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:56,277 INFO  [root] No of ion clusters:18 (Memory usage:260MB)
2021-11-17 15:36:56,277 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_971_974_PeakCluster.serFS...
2021-11-17 15:36:56,278 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:56,737 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:57,069 INFO  [root] ==================================================================================
2021-11-17 15:36:57,069 INFO  [root] Processing DIA MS2 (mz range):968.0_971.0( 4/61 )
2021-11-17 15:36:57,119 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:57,119 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:57,806 INFO  [root] 128595 Peak curves found (Memory usage:240MB)
2021-11-17 15:36:57,808 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:57,808 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:36:58,245 INFO  [root] No of ion clusters:23 (Memory usage:250MB)
2021-11-17 15:36:58,245 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_968_971_PeakCluster.serFS...
2021-11-17 15:36:58,246 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:36:58,511 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:36:58,807 INFO  [root] ==================================================================================
2021-11-17 15:36:58,807 INFO  [root] Processing DIA MS2 (mz range):965.0_968.0( 5/61 )
2021-11-17 15:36:58,858 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:36:58,858 INFO  [root] Smoothing detected signals......
2021-11-17 15:36:59,550 INFO  [root] 139139 Peak curves found (Memory usage:245MB)
2021-11-17 15:36:59,552 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:36:59,552 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:00,000 INFO  [root] No of ion clusters:20 (Memory usage:255MB)
2021-11-17 15:37:00,000 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_965_968_PeakCluster.serFS...
2021-11-17 15:37:00,001 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:00,274 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:00,558 INFO  [root] ==================================================================================
2021-11-17 15:37:00,558 INFO  [root] Processing DIA MS2 (mz range):962.0_965.0( 6/61 )
2021-11-17 15:37:00,611 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:00,612 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:01,628 INFO  [root] 156053 Peak curves found (Memory usage:254MB)
2021-11-17 15:37:01,632 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:01,632 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:02,126 INFO  [root] No of ion clusters:20 (Memory usage:266MB)
2021-11-17 15:37:02,127 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_962_965_PeakCluster.serFS...
2021-11-17 15:37:02,127 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:02,495 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:02,789 INFO  [root] ==================================================================================
2021-11-17 15:37:02,789 INFO  [root] Processing DIA MS2 (mz range):959.0_962.0( 7/61 )
2021-11-17 15:37:02,845 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:02,845 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:03,838 INFO  [root] 155655 Peak curves found (Memory usage:255MB)
2021-11-17 15:37:03,840 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:03,840 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:04,323 INFO  [root] No of ion clusters:19 (Memory usage:266MB)
2021-11-17 15:37:04,323 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_959_962_PeakCluster.serFS...
2021-11-17 15:37:04,324 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:04,627 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:04,901 INFO  [root] ==================================================================================
2021-11-17 15:37:04,902 INFO  [root] Processing DIA MS2 (mz range):956.0_959.0( 8/61 )
2021-11-17 15:37:04,958 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:04,959 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:05,923 INFO  [root] 174991 Peak curves found (Memory usage:263MB)
2021-11-17 15:37:05,925 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:05,925 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:06,437 INFO  [root] No of ion clusters:20 (Memory usage:276MB)
2021-11-17 15:37:06,438 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_956_959_PeakCluster.serFS...
2021-11-17 15:37:06,438 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:06,714 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:07,034 INFO  [root] ==================================================================================
2021-11-17 15:37:07,034 INFO  [root] Processing DIA MS2 (mz range):953.0_956.0( 9/61 )
2021-11-17 15:37:07,114 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:07,114 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:09,748 INFO  [root] 179780 Peak curves found (Memory usage:270MB)
2021-11-17 15:37:09,749 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:09,749 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:10,285 INFO  [root] No of ion clusters:34 (Memory usage:284MB)
2021-11-17 15:37:10,285 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_953_956_PeakCluster.serFS...
2021-11-17 15:37:10,286 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:10,637 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:10,927 INFO  [root] ==================================================================================
2021-11-17 15:37:10,927 INFO  [root] Processing DIA MS2 (mz range):950.0_953.0( 10/61 )
2021-11-17 15:37:10,988 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:10,988 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:12,364 INFO  [root] 190371 Peak curves found (Memory usage:273MB)
2021-11-17 15:37:12,365 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:12,365 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:12,926 INFO  [root] No of ion clusters:18 (Memory usage:288MB)
2021-11-17 15:37:12,926 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_950_953_PeakCluster.serFS...
2021-11-17 15:37:12,927 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:13,304 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:13,593 INFO  [root] ==================================================================================
2021-11-17 15:37:13,593 INFO  [root] Processing DIA MS2 (mz range):947.0_950.0( 11/61 )
2021-11-17 15:37:13,662 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:13,662 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:14,689 INFO  [root] 181354 Peak curves found (Memory usage:270MB)
2021-11-17 15:37:14,691 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:14,691 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:15,265 INFO  [root] No of ion clusters:27 (Memory usage:285MB)
2021-11-17 15:37:15,265 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_947_950_PeakCluster.serFS...
2021-11-17 15:37:15,266 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:15,630 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:15,949 INFO  [root] ==================================================================================
2021-11-17 15:37:15,950 INFO  [root] Processing DIA MS2 (mz range):944.0_947.0( 12/61 )
2021-11-17 15:37:16,007 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:16,007 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:16,978 INFO  [root] 173662 Peak curves found (Memory usage:269MB)
2021-11-17 15:37:16,979 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:16,979 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:17,499 INFO  [root] No of ion clusters:22 (Memory usage:282MB)
2021-11-17 15:37:17,499 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_944_947_PeakCluster.serFS...
2021-11-17 15:37:17,500 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:17,889 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:18,191 INFO  [root] ==================================================================================
2021-11-17 15:37:18,191 INFO  [root] Processing DIA MS2 (mz range):941.0_944.0( 13/61 )
2021-11-17 15:37:18,250 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:18,250 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:19,537 INFO  [root] 175815 Peak curves found (Memory usage:271MB)
2021-11-17 15:37:19,539 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:19,539 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:20,102 INFO  [root] No of ion clusters:18 (Memory usage:284MB)
2021-11-17 15:37:20,102 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_941_944_PeakCluster.serFS...
2021-11-17 15:37:20,103 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:20,430 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:20,705 INFO  [root] ==================================================================================
2021-11-17 15:37:20,706 INFO  [root] Processing DIA MS2 (mz range):938.0_941.0( 14/61 )
2021-11-17 15:37:20,772 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:20,772 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:22,706 INFO  [root] 195426 Peak curves found (Memory usage:281MB)
2021-11-17 15:37:22,708 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:22,708 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:23,288 INFO  [root] No of ion clusters:21 (Memory usage:296MB)
2021-11-17 15:37:23,288 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_938_941_PeakCluster.serFS...
2021-11-17 15:37:23,289 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:23,652 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:23,947 INFO  [root] ==================================================================================
2021-11-17 15:37:23,948 INFO  [root] Processing DIA MS2 (mz range):935.0_938.0( 15/61 )
2021-11-17 15:37:24,015 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:24,015 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:26,175 INFO  [root] 189900 Peak curves found (Memory usage:280MB)
2021-11-17 15:37:26,177 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:26,177 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:26,729 INFO  [root] No of ion clusters:25 (Memory usage:295MB)
2021-11-17 15:37:26,729 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_935_938_PeakCluster.serFS...
2021-11-17 15:37:26,729 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:27,211 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:27,566 INFO  [root] ==================================================================================
2021-11-17 15:37:27,566 INFO  [root] Processing DIA MS2 (mz range):932.0_935.0( 16/61 )
2021-11-17 15:37:27,620 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:27,620 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:28,702 INFO  [root] 162886 Peak curves found (Memory usage:270MB)
2021-11-17 15:37:28,703 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:28,703 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:29,205 INFO  [root] No of ion clusters:20 (Memory usage:282MB)
2021-11-17 15:37:29,205 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_932_935_PeakCluster.serFS...
2021-11-17 15:37:29,206 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:29,608 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:29,908 INFO  [root] ==================================================================================
2021-11-17 15:37:29,908 INFO  [root] Processing DIA MS2 (mz range):929.0_932.0( 17/61 )
2021-11-17 15:37:29,959 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:29,959 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:30,692 INFO  [root] 151260 Peak curves found (Memory usage:265MB)
2021-11-17 15:37:30,694 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:30,694 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:31,203 INFO  [root] No of ion clusters:22 (Memory usage:276MB)
2021-11-17 15:37:31,203 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_929_932_PeakCluster.serFS...
2021-11-17 15:37:31,204 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:31,485 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:31,780 INFO  [root] ==================================================================================
2021-11-17 15:37:31,780 INFO  [root] Processing DIA MS2 (mz range):926.0_929.0( 18/61 )
2021-11-17 15:37:31,830 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:31,830 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:32,678 INFO  [root] 142983 Peak curves found (Memory usage:263MB)
2021-11-17 15:37:32,680 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:32,680 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:33,137 INFO  [root] No of ion clusters:18 (Memory usage:274MB)
2021-11-17 15:37:33,137 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_926_929_PeakCluster.serFS...
2021-11-17 15:37:33,138 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:33,416 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:33,822 INFO  [root] ==================================================================================
2021-11-17 15:37:33,822 INFO  [root] Processing DIA MS2 (mz range):923.0_926.0( 19/61 )
2021-11-17 15:37:33,878 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:33,878 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:34,707 INFO  [root] 145285 Peak curves found (Memory usage:264MB)
2021-11-17 15:37:34,709 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:34,709 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:35,172 INFO  [root] No of ion clusters:14 (Memory usage:275MB)
2021-11-17 15:37:35,172 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_923_926_PeakCluster.serFS...
2021-11-17 15:37:35,173 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:35,453 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:35,730 INFO  [root] ==================================================================================
2021-11-17 15:37:35,730 INFO  [root] Processing DIA MS2 (mz range):920.0_923.0( 20/61 )
2021-11-17 15:37:35,783 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:35,783 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:36,572 INFO  [root] 161365 Peak curves found (Memory usage:271MB)
2021-11-17 15:37:36,574 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:36,574 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:37,082 INFO  [root] No of ion clusters:19 (Memory usage:283MB)
2021-11-17 15:37:37,082 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_920_923_PeakCluster.serFS...
2021-11-17 15:37:37,083 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:37,373 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:37,596 INFO  [root] ==================================================================================
2021-11-17 15:37:37,596 INFO  [root] Processing DIA MS2 (mz range):917.0_920.0( 21/61 )
2021-11-17 15:37:37,684 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:37,684 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:39,027 INFO  [root] 145769 Peak curves found (Memory usage:266MB)
2021-11-17 15:37:39,029 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:39,029 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:39,475 INFO  [root] No of ion clusters:24 (Memory usage:277MB)
2021-11-17 15:37:39,475 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_917_920_PeakCluster.serFS...
2021-11-17 15:37:39,476 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:39,807 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:40,094 INFO  [root] ==================================================================================
2021-11-17 15:37:40,094 INFO  [root] Processing DIA MS2 (mz range):914.0_917.0( 22/61 )
2021-11-17 15:37:40,145 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:40,145 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:40,875 INFO  [root] 148783 Peak curves found (Memory usage:265MB)
2021-11-17 15:37:40,877 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:40,877 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:41,436 INFO  [root] No of ion clusters:19 (Memory usage:277MB)
2021-11-17 15:37:41,436 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_914_917_PeakCluster.serFS...
2021-11-17 15:37:41,437 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:41,673 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:41,999 INFO  [root] ==================================================================================
2021-11-17 15:37:41,999 INFO  [root] Processing DIA MS2 (mz range):911.0_914.0( 23/61 )
2021-11-17 15:37:42,047 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:42,048 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:42,880 INFO  [root] 130806 Peak curves found (Memory usage:260MB)
2021-11-17 15:37:42,882 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:42,882 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:43,306 INFO  [root] No of ion clusters:27 (Memory usage:270MB)
2021-11-17 15:37:43,306 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_911_914_PeakCluster.serFS...
2021-11-17 15:37:43,307 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:43,576 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:43,868 INFO  [root] ==================================================================================
2021-11-17 15:37:43,868 INFO  [root] Processing DIA MS2 (mz range):908.0_911.0( 24/61 )
2021-11-17 15:37:43,921 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:43,921 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:44,735 INFO  [root] 136230 Peak curves found (Memory usage:263MB)
2021-11-17 15:37:44,737 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:44,737 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:45,219 INFO  [root] No of ion clusters:25 (Memory usage:273MB)
2021-11-17 15:37:45,219 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_908_911_PeakCluster.serFS...
2021-11-17 15:37:45,221 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:45,477 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:45,765 INFO  [root] ==================================================================================
2021-11-17 15:37:45,765 INFO  [root] Processing DIA MS2 (mz range):905.0_908.0( 25/61 )
2021-11-17 15:37:45,807 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:45,807 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:46,443 INFO  [root] 132989 Peak curves found (Memory usage:261MB)
2021-11-17 15:37:46,445 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:46,445 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:46,999 INFO  [root] No of ion clusters:26 (Memory usage:271MB)
2021-11-17 15:37:46,999 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_905_908_PeakCluster.serFS...
2021-11-17 15:37:47,000 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:47,199 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:47,486 INFO  [root] ==================================================================================
2021-11-17 15:37:47,486 INFO  [root] Processing DIA MS2 (mz range):902.0_905.0( 26/61 )
2021-11-17 15:37:47,546 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:47,546 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:48,286 INFO  [root] 149255 Peak curves found (Memory usage:268MB)
2021-11-17 15:37:48,288 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:48,288 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:48,737 INFO  [root] No of ion clusters:29 (Memory usage:280MB)
2021-11-17 15:37:48,737 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_902_905_PeakCluster.serFS...
2021-11-17 15:37:48,738 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:49,011 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:49,281 INFO  [root] ==================================================================================
2021-11-17 15:37:49,281 INFO  [root] Processing DIA MS2 (mz range):899.0_902.0( 27/61 )
2021-11-17 15:37:49,333 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:49,333 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:50,582 INFO  [root] 146478 Peak curves found (Memory usage:270MB)
2021-11-17 15:37:50,584 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:50,584 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:51,090 INFO  [root] No of ion clusters:18 (Memory usage:281MB)
2021-11-17 15:37:51,090 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_899_902_PeakCluster.serFS...
2021-11-17 15:37:51,091 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:51,363 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:51,628 INFO  [root] ==================================================================================
2021-11-17 15:37:51,628 INFO  [root] Processing DIA MS2 (mz range):896.0_899.0( 28/61 )
2021-11-17 15:37:51,716 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:51,717 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:52,473 INFO  [root] 160679 Peak curves found (Memory usage:274MB)
2021-11-17 15:37:52,474 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:52,474 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:52,950 INFO  [root] No of ion clusters:37 (Memory usage:286MB)
2021-11-17 15:37:52,951 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_896_899_PeakCluster.serFS...
2021-11-17 15:37:52,951 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:53,218 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:53,524 INFO  [root] ==================================================================================
2021-11-17 15:37:53,524 INFO  [root] Processing DIA MS2 (mz range):893.0_896.0( 29/61 )
2021-11-17 15:37:53,579 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:53,579 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:54,399 INFO  [root] 151253 Peak curves found (Memory usage:271MB)
2021-11-17 15:37:54,401 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:54,402 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:54,864 INFO  [root] No of ion clusters:28 (Memory usage:283MB)
2021-11-17 15:37:54,864 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_893_896_PeakCluster.serFS...
2021-11-17 15:37:54,865 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:55,283 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:55,569 INFO  [root] ==================================================================================
2021-11-17 15:37:55,569 INFO  [root] Processing DIA MS2 (mz range):890.0_893.0( 30/61 )
2021-11-17 15:37:55,629 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:55,629 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:56,397 INFO  [root] 153127 Peak curves found (Memory usage:271MB)
2021-11-17 15:37:56,399 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:56,399 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:56,892 INFO  [root] No of ion clusters:16 (Memory usage:282MB)
2021-11-17 15:37:56,893 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_890_893_PeakCluster.serFS...
2021-11-17 15:37:56,893 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:57,148 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:57,426 INFO  [root] ==================================================================================
2021-11-17 15:37:57,426 INFO  [root] Processing DIA MS2 (mz range):887.0_890.0( 31/61 )
2021-11-17 15:37:57,488 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:57,488 INFO  [root] Smoothing detected signals......
2021-11-17 15:37:58,296 INFO  [root] 151147 Peak curves found (Memory usage:272MB)
2021-11-17 15:37:58,299 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:37:58,299 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:37:58,771 INFO  [root] No of ion clusters:24 (Memory usage:283MB)
2021-11-17 15:37:58,771 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_887_890_PeakCluster.serFS...
2021-11-17 15:37:58,771 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:37:59,102 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:37:59,388 INFO  [root] ==================================================================================
2021-11-17 15:37:59,388 INFO  [root] Processing DIA MS2 (mz range):884.0_887.0( 32/61 )
2021-11-17 15:37:59,440 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:37:59,440 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:00,232 INFO  [root] 159417 Peak curves found (Memory usage:275MB)
2021-11-17 15:38:00,235 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:00,235 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:00,766 INFO  [root] No of ion clusters:34 (Memory usage:286MB)
2021-11-17 15:38:00,766 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_884_887_PeakCluster.serFS...
2021-11-17 15:38:00,766 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:01,045 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:01,388 INFO  [root] ==================================================================================
2021-11-17 15:38:01,388 INFO  [root] Processing DIA MS2 (mz range):881.0_884.0( 33/61 )
2021-11-17 15:38:01,454 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:01,455 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:02,294 INFO  [root] 164034 Peak curves found (Memory usage:276MB)
2021-11-17 15:38:02,296 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:02,296 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:02,834 INFO  [root] No of ion clusters:22 (Memory usage:289MB)
2021-11-17 15:38:02,834 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_881_884_PeakCluster.serFS...
2021-11-17 15:38:02,834 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:03,136 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:03,404 INFO  [root] ==================================================================================
2021-11-17 15:38:03,404 INFO  [root] Processing DIA MS2 (mz range):878.0_881.0( 34/61 )
2021-11-17 15:38:03,459 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:03,459 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:04,276 INFO  [root] 170028 Peak curves found (Memory usage:280MB)
2021-11-17 15:38:04,278 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:04,278 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:04,841 INFO  [root] No of ion clusters:29 (Memory usage:293MB)
2021-11-17 15:38:04,841 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_878_881_PeakCluster.serFS...
2021-11-17 15:38:04,842 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:05,198 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:05,494 INFO  [root] ==================================================================================
2021-11-17 15:38:05,494 INFO  [root] Processing DIA MS2 (mz range):875.0_878.0( 35/61 )
2021-11-17 15:38:05,550 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:05,550 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:06,674 INFO  [root] 183862 Peak curves found (Memory usage:286MB)
2021-11-17 15:38:06,676 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:06,676 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:07,224 INFO  [root] No of ion clusters:16 (Memory usage:300MB)
2021-11-17 15:38:07,224 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_875_878_PeakCluster.serFS...
2021-11-17 15:38:07,225 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:07,632 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:07,900 INFO  [root] ==================================================================================
2021-11-17 15:38:07,900 INFO  [root] Processing DIA MS2 (mz range):872.0_875.0( 36/61 )
2021-11-17 15:38:07,970 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:07,970 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:09,362 INFO  [root] 182692 Peak curves found (Memory usage:288MB)
2021-11-17 15:38:09,364 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:09,364 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:09,963 INFO  [root] No of ion clusters:29 (Memory usage:302MB)
2021-11-17 15:38:09,964 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_872_875_PeakCluster.serFS...
2021-11-17 15:38:09,964 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:10,521 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:10,893 INFO  [root] ==================================================================================
2021-11-17 15:38:10,893 INFO  [root] Processing DIA MS2 (mz range):869.0_872.0( 37/61 )
2021-11-17 15:38:10,957 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:10,957 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:11,815 INFO  [root] 174334 Peak curves found (Memory usage:281MB)
2021-11-17 15:38:11,817 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:11,817 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:12,323 INFO  [root] No of ion clusters:16 (Memory usage:295MB)
2021-11-17 15:38:12,324 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_869_872_PeakCluster.serFS...
2021-11-17 15:38:12,324 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:12,672 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:12,989 INFO  [root] ==================================================================================
2021-11-17 15:38:12,989 INFO  [root] Processing DIA MS2 (mz range):866.0_869.0( 38/61 )
2021-11-17 15:38:13,055 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:13,055 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:13,881 INFO  [root] 160413 Peak curves found (Memory usage:276MB)
2021-11-17 15:38:13,883 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:13,883 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:14,418 INFO  [root] No of ion clusters:24 (Memory usage:288MB)
2021-11-17 15:38:14,418 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_866_869_PeakCluster.serFS...
2021-11-17 15:38:14,419 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:14,727 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:15,034 INFO  [root] ==================================================================================
2021-11-17 15:38:15,035 INFO  [root] Processing DIA MS2 (mz range):863.0_866.0( 39/61 )
2021-11-17 15:38:15,091 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:15,091 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:16,011 INFO  [root] 164937 Peak curves found (Memory usage:280MB)
2021-11-17 15:38:16,014 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:16,014 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:16,537 INFO  [root] No of ion clusters:20 (Memory usage:292MB)
2021-11-17 15:38:16,537 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_863_866_PeakCluster.serFS...
2021-11-17 15:38:16,539 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:16,927 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:17,246 INFO  [root] ==================================================================================
2021-11-17 15:38:17,246 INFO  [root] Processing DIA MS2 (mz range):860.0_863.0( 40/61 )
2021-11-17 15:38:17,305 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:17,305 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:18,300 INFO  [root] 180371 Peak curves found (Memory usage:287MB)
2021-11-17 15:38:18,301 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:18,301 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:18,897 INFO  [root] No of ion clusters:24 (Memory usage:301MB)
2021-11-17 15:38:18,897 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_860_863_PeakCluster.serFS...
2021-11-17 15:38:18,898 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:19,372 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:19,696 INFO  [root] ==================================================================================
2021-11-17 15:38:19,696 INFO  [root] Processing DIA MS2 (mz range):857.0_860.0( 41/61 )
2021-11-17 15:38:19,772 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:19,772 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:20,946 INFO  [root] 197811 Peak curves found (Memory usage:293MB)
2021-11-17 15:38:20,948 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:20,948 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:21,510 INFO  [root] No of ion clusters:14 (Memory usage:309MB)
2021-11-17 15:38:21,510 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_857_860_PeakCluster.serFS...
2021-11-17 15:38:21,511 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:21,915 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:22,229 INFO  [root] ==================================================================================
2021-11-17 15:38:22,229 INFO  [root] Processing DIA MS2 (mz range):854.0_857.0( 42/61 )
2021-11-17 15:38:22,308 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:22,308 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:23,586 INFO  [root] 199631 Peak curves found (Memory usage:296MB)
2021-11-17 15:38:23,588 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:23,588 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:24,211 INFO  [root] No of ion clusters:27 (Memory usage:311MB)
2021-11-17 15:38:24,211 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_854_857_PeakCluster.serFS...
2021-11-17 15:38:24,212 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:24,746 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:25,103 INFO  [root] ==================================================================================
2021-11-17 15:38:25,104 INFO  [root] Processing DIA MS2 (mz range):851.0_854.0( 43/61 )
2021-11-17 15:38:25,174 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:25,174 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:26,277 INFO  [root] 211518 Peak curves found (Memory usage:298MB)
2021-11-17 15:38:26,279 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:26,279 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:26,891 INFO  [root] No of ion clusters:18 (Memory usage:314MB)
2021-11-17 15:38:26,891 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_851_854_PeakCluster.serFS...
2021-11-17 15:38:26,891 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:27,274 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:27,573 INFO  [root] ==================================================================================
2021-11-17 15:38:27,573 INFO  [root] Processing DIA MS2 (mz range):848.0_851.0( 44/61 )
2021-11-17 15:38:27,633 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:27,633 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:28,979 INFO  [root] 184951 Peak curves found (Memory usage:290MB)
2021-11-17 15:38:28,981 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:28,982 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:29,566 INFO  [root] No of ion clusters:16 (Memory usage:304MB)
2021-11-17 15:38:29,566 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_848_851_PeakCluster.serFS...
2021-11-17 15:38:29,567 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:30,133 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:30,468 INFO  [root] ==================================================================================
2021-11-17 15:38:30,468 INFO  [root] Processing DIA MS2 (mz range):845.0_848.0( 45/61 )
2021-11-17 15:38:30,543 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:30,543 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:31,561 INFO  [root] 197630 Peak curves found (Memory usage:294MB)
2021-11-17 15:38:31,563 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:31,563 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:32,178 INFO  [root] No of ion clusters:12 (Memory usage:310MB)
2021-11-17 15:38:32,178 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_845_848_PeakCluster.serFS...
2021-11-17 15:38:32,179 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:32,611 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:32,904 INFO  [root] ==================================================================================
2021-11-17 15:38:32,904 INFO  [root] Processing DIA MS2 (mz range):842.0_845.0( 46/61 )
2021-11-17 15:38:32,964 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:32,964 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:33,894 INFO  [root] 175699 Peak curves found (Memory usage:287MB)
2021-11-17 15:38:33,897 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:33,897 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:34,421 INFO  [root] No of ion clusters:28 (Memory usage:301MB)
2021-11-17 15:38:34,421 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_842_845_PeakCluster.serFS...
2021-11-17 15:38:34,422 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:34,946 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:35,255 INFO  [root] ==================================================================================
2021-11-17 15:38:35,255 INFO  [root] Processing DIA MS2 (mz range):839.0_842.0( 47/61 )
2021-11-17 15:38:35,317 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:35,317 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:36,300 INFO  [root] 203118 Peak curves found (Memory usage:298MB)
2021-11-17 15:38:36,302 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:36,302 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:36,929 INFO  [root] No of ion clusters:20 (Memory usage:314MB)
2021-11-17 15:38:36,929 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_839_842_PeakCluster.serFS...
2021-11-17 15:38:36,931 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:37,418 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:37,730 INFO  [root] ==================================================================================
2021-11-17 15:38:37,730 INFO  [root] Processing DIA MS2 (mz range):836.0_839.0( 48/61 )
2021-11-17 15:38:37,817 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:37,817 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:39,435 INFO  [root] 225166 Peak curves found (Memory usage:308MB)
2021-11-17 15:38:39,437 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:39,437 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:40,112 INFO  [root] No of ion clusters:20 (Memory usage:326MB)
2021-11-17 15:38:40,112 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_836_839_PeakCluster.serFS...
2021-11-17 15:38:40,113 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:40,793 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:41,169 INFO  [root] ==================================================================================
2021-11-17 15:38:41,169 INFO  [root] Processing DIA MS2 (mz range):833.0_836.0( 49/61 )
2021-11-17 15:38:41,249 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:41,249 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:42,824 INFO  [root] 214970 Peak curves found (Memory usage:305MB)
2021-11-17 15:38:42,826 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:42,826 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:43,507 INFO  [root] No of ion clusters:16 (Memory usage:321MB)
2021-11-17 15:38:43,507 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_833_836_PeakCluster.serFS...
2021-11-17 15:38:43,508 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:44,102 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:44,430 INFO  [root] ==================================================================================
2021-11-17 15:38:44,430 INFO  [root] Processing DIA MS2 (mz range):830.0_833.0( 50/61 )
2021-11-17 15:38:44,510 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:44,510 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:45,650 INFO  [root] 217800 Peak curves found (Memory usage:305MB)
2021-11-17 15:38:45,652 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:45,652 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:46,287 INFO  [root] No of ion clusters:21 (Memory usage:322MB)
2021-11-17 15:38:46,287 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_830_833_PeakCluster.serFS...
2021-11-17 15:38:46,288 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:46,865 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:47,226 INFO  [root] ==================================================================================
2021-11-17 15:38:47,226 INFO  [root] Processing DIA MS2 (mz range):827.0_830.0( 51/61 )
2021-11-17 15:38:47,299 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:47,299 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:48,692 INFO  [root] 233545 Peak curves found (Memory usage:313MB)
2021-11-17 15:38:48,694 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:48,694 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:49,319 INFO  [root] No of ion clusters:17 (Memory usage:330MB)
2021-11-17 15:38:49,319 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_827_830_PeakCluster.serFS...
2021-11-17 15:38:49,320 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:49,874 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:50,187 INFO  [root] ==================================================================================
2021-11-17 15:38:50,187 INFO  [root] Processing DIA MS2 (mz range):824.0_827.0( 52/61 )
2021-11-17 15:38:50,262 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:50,262 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:52,049 INFO  [root] 214947 Peak curves found (Memory usage:307MB)
2021-11-17 15:38:52,051 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:52,051 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:52,649 INFO  [root] No of ion clusters:16 (Memory usage:324MB)
2021-11-17 15:38:52,649 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_824_827_PeakCluster.serFS...
2021-11-17 15:38:52,649 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:53,274 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:53,588 INFO  [root] ==================================================================================
2021-11-17 15:38:53,588 INFO  [root] Processing DIA MS2 (mz range):821.0_824.0( 53/61 )
2021-11-17 15:38:53,656 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:53,656 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:54,702 INFO  [root] 215290 Peak curves found (Memory usage:306MB)
2021-11-17 15:38:54,704 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:54,704 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:55,344 INFO  [root] No of ion clusters:22 (Memory usage:322MB)
2021-11-17 15:38:55,344 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_821_824_PeakCluster.serFS...
2021-11-17 15:38:55,347 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:55,828 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:56,147 INFO  [root] ==================================================================================
2021-11-17 15:38:56,147 INFO  [root] Processing DIA MS2 (mz range):818.0_821.0( 54/61 )
2021-11-17 15:38:56,220 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:56,220 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:57,329 INFO  [root] 181692 Peak curves found (Memory usage:294MB)
2021-11-17 15:38:57,330 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:57,330 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:38:57,897 INFO  [root] No of ion clusters:16 (Memory usage:308MB)
2021-11-17 15:38:57,897 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_818_821_PeakCluster.serFS...
2021-11-17 15:38:57,898 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:38:58,356 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:38:58,646 INFO  [root] ==================================================================================
2021-11-17 15:38:58,646 INFO  [root] Processing DIA MS2 (mz range):815.0_818.0( 55/61 )
2021-11-17 15:38:58,706 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:38:58,706 INFO  [root] Smoothing detected signals......
2021-11-17 15:38:59,652 INFO  [root] 179166 Peak curves found (Memory usage:293MB)
2021-11-17 15:38:59,654 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:38:59,654 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:00,178 INFO  [root] No of ion clusters:12 (Memory usage:307MB)
2021-11-17 15:39:00,178 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_815_818_PeakCluster.serFS...
2021-11-17 15:39:00,179 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:00,606 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:00,892 INFO  [root] ==================================================================================
2021-11-17 15:39:00,892 INFO  [root] Processing DIA MS2 (mz range):812.0_815.0( 56/61 )
2021-11-17 15:39:00,953 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:00,953 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:02,244 INFO  [root] 170028 Peak curves found (Memory usage:291MB)
2021-11-17 15:39:02,246 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:02,246 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:02,775 INFO  [root] No of ion clusters:22 (Memory usage:304MB)
2021-11-17 15:39:02,775 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_812_815_PeakCluster.serFS...
2021-11-17 15:39:02,776 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:03,196 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:03,509 INFO  [root] ==================================================================================
2021-11-17 15:39:03,510 INFO  [root] Processing DIA MS2 (mz range):809.0_812.0( 57/61 )
2021-11-17 15:39:03,567 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:03,567 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:04,506 INFO  [root] 180782 Peak curves found (Memory usage:294MB)
2021-11-17 15:39:04,508 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:04,508 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:05,036 INFO  [root] No of ion clusters:20 (Memory usage:308MB)
2021-11-17 15:39:05,036 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_809_812_PeakCluster.serFS...
2021-11-17 15:39:05,036 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:05,405 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:05,705 INFO  [root] ==================================================================================
2021-11-17 15:39:05,705 INFO  [root] Processing DIA MS2 (mz range):806.0_809.0( 58/61 )
2021-11-17 15:39:05,763 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:05,763 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:06,820 INFO  [root] 171888 Peak curves found (Memory usage:292MB)
2021-11-17 15:39:06,822 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:06,822 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:07,340 INFO  [root] No of ion clusters:33 (Memory usage:305MB)
2021-11-17 15:39:07,340 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_806_809_PeakCluster.serFS...
2021-11-17 15:39:07,341 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:07,861 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:08,180 INFO  [root] ==================================================================================
2021-11-17 15:39:08,180 INFO  [root] Processing DIA MS2 (mz range):803.0_806.0( 59/61 )
2021-11-17 15:39:08,243 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:08,243 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:09,269 INFO  [root] 197288 Peak curves found (Memory usage:302MB)
2021-11-17 15:39:09,271 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:09,271 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:09,860 INFO  [root] No of ion clusters:17 (Memory usage:317MB)
2021-11-17 15:39:09,860 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_803_806_PeakCluster.serFS...
2021-11-17 15:39:09,861 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:10,321 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:10,642 INFO  [root] ==================================================================================
2021-11-17 15:39:10,642 INFO  [root] Processing DIA MS2 (mz range):800.0_803.0( 60/61 )
2021-11-17 15:39:10,695 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:10,695 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:11,878 INFO  [root] 107797 Peak curves found (Memory usage:270MB)
2021-11-17 15:39:11,880 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:11,880 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:12,257 INFO  [root] No of ion clusters:19 (Memory usage:277MB)
2021-11-17 15:39:12,257 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_800_803_PeakCluster.serFS...
2021-11-17 15:39:12,258 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:12,635 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:12,932 INFO  [root] ==================================================================================
2021-11-17 15:39:12,932 INFO  [root] Processing DIA MS2 (mz range):797.0_800.0( 61/61 )
2021-11-17 15:39:12,963 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:12,963 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:14,225 INFO  [root] 93308 Peak curves found (Memory usage:268MB)
2021-11-17 15:39:14,227 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:14,227 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:14,605 INFO  [root] No of ion clusters:93 (Memory usage:275MB)
2021-11-17 15:39:14,605 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_797_800_PeakCluster.serFS...
2021-11-17 15:39:14,606 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:15,547 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:16,209 INFO  [root] ==================================================================================
2021-11-17 15:39:18,048 INFO  [root] C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.mzXML processed time:0 hour, 2 min, 51 sec
2021-11-17 15:39:18,048 INFO  [root] Job complete
2021-11-17 15:39:18,048 INFO  [root] =================================================================================================
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
=================================================================================================
DIA-Umpire singal extraction analysis  (version: v2.2.3)
(c) University of Michigan
2021-11-17 15:39:25,290 INFO  [root] Version: v2.2.3
2021-11-17 15:39:25,291 INFO  [root] Parameter file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
2021-11-17 15:39:25,291 INFO  [root] Spectra file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.mzXML
2021-11-17 15:39:25,293 INFO  [root] 
2021-11-17 15:39:25,293 INFO  [root] ####################################################################################################
2021-11-17 15:39:25,293 INFO  [root] #No of threads
2021-11-17 15:39:25,295 INFO  [root] Thread = 7
2021-11-17 15:39:25,295 INFO  [root] ####################################################################################################
2021-11-17 15:39:25,295 INFO  [root] 
2021-11-17 15:39:25,295 INFO  [root] ## omit Thread
2021-11-17 15:39:25,295 INFO  [root] 
2021-11-17 15:39:25,295 INFO  [root] #Precursor-fragments grouping parameters
2021-11-17 15:39:25,295 INFO  [root] RPmax = 25
2021-11-17 15:39:25,295 INFO  [root] RFmax = 500
2021-11-17 15:39:25,295 INFO  [root] CorrThreshold = 0
2021-11-17 15:39:25,296 INFO  [root] DeltaApex = 0.2
2021-11-17 15:39:25,296 INFO  [root] RTOverlap = 0.3
2021-11-17 15:39:25,296 INFO  [root] 
2021-11-17 15:39:25,296 INFO  [root] #Fragment intensity adjustments
2021-11-17 15:39:25,296 INFO  [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2021-11-17 15:39:25,296 INFO  [root] AdjustFragIntensity = true
2021-11-17 15:39:25,296 INFO  [root] BoostComplementaryIon = false
2021-11-17 15:39:25,296 INFO  [root] 
2021-11-17 15:39:25,296 INFO  [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2021-11-17 15:39:25,296 INFO  [root] ExportPrecursorPeak = false
2021-11-17 15:39:25,296 INFO  [root] 
2021-11-17 15:39:25,296 INFO  [root] Q1 = true
2021-11-17 15:39:25,296 INFO  [root] Q2 = true
2021-11-17 15:39:25,297 INFO  [root] Q3 = true
2021-11-17 15:39:25,297 INFO  [root] 
2021-11-17 15:39:25,297 INFO  [root] #Signal extraction: mass accuracy and resolution
2021-11-17 15:39:25,297 INFO  [root] # resolution parameter matters only for data generated in profile mode
2021-11-17 15:39:25,297 INFO  [root] SE.MS1PPM = 10
2021-11-17 15:39:25,297 INFO  [root] SE.MS2PPM = 10
2021-11-17 15:39:25,297 INFO  [root] SE.Resolution = 60000
2021-11-17 15:39:25,297 INFO  [root] 
2021-11-17 15:39:25,297 INFO  [root] #Signal extraction: signal to noise filter
2021-11-17 15:39:25,297 INFO  [root] SE.SN = 1.1
2021-11-17 15:39:25,297 INFO  [root] SE.MS2SN = 1.1
2021-11-17 15:39:25,297 INFO  [root] 
2021-11-17 15:39:25,297 INFO  [root] #Signal extraction: minimum signal intensity filter
2021-11-17 15:39:25,297 INFO  [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2021-11-17 15:39:25,297 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2021-11-17 15:39:25,297 INFO  [root] SE.EstimateBG = false
2021-11-17 15:39:25,297 INFO  [root] SE.MinMSIntensity = 1
2021-11-17 15:39:25,298 INFO  [root] SE.MinMSMSIntensity = 1
2021-11-17 15:39:25,298 INFO  [root] 
2021-11-17 15:39:25,298 INFO  [root] #Signal extraction: peak curve detection and isotope grouping
2021-11-17 15:39:25,298 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2021-11-17 15:39:25,298 INFO  [root] SE.NoMissedScan = 1
2021-11-17 15:39:25,298 INFO  [root] SE.MaxCurveRTRange = 2
2021-11-17 15:39:25,298 INFO  [root] SE.RemoveGroupedPeaks = true
2021-11-17 15:39:25,298 INFO  [root] SE.RemoveGroupedPeaksRTOverlap = 0.3
2021-11-17 15:39:25,298 INFO  [root] SE.RemoveGroupedPeaksCorr = 0.3
2021-11-17 15:39:25,298 INFO  [root] SE.MinNoPeakCluster = 2
2021-11-17 15:39:25,298 INFO  [root] SE.MaxNoPeakCluster = 4
2021-11-17 15:39:25,480 INFO  [root] 
2021-11-17 15:39:25,480 INFO  [root] #Signal extraction: filtering of MS1 features
2021-11-17 15:39:25,480 INFO  [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2021-11-17 15:39:25,481 INFO  [root] SE.IsoPattern = 0.3
2021-11-17 15:39:25,481 INFO  [root] SE.MassDefectFilter = false
2021-11-17 15:39:25,481 INFO  [root] SE.MassDefectOffset = 0.1
2021-11-17 15:39:25,481 INFO  [root] 
2021-11-17 15:39:25,481 INFO  [root] #Signal extraction: other
2021-11-17 15:39:25,482 INFO  [root] SE.StartCharge = 1
2021-11-17 15:39:25,482 INFO  [root] SE.EndCharge = 5
2021-11-17 15:39:25,482 INFO  [root] SE.MS2StartCharge = 2
2021-11-17 15:39:25,482 INFO  [root] SE.MS2EndCharge = 5
2021-11-17 15:39:25,482 INFO  [root] SE.MinFrag = 10
2021-11-17 15:39:25,482 INFO  [root] SE.StartRT = 0
2021-11-17 15:39:25,482 INFO  [root] SE.EndRT = 9999
2021-11-17 15:39:25,483 INFO  [root] SE.MinMZ = 200
2021-11-17 15:39:25,483 INFO  [root] SE.MinPrecursorMass = 600
2021-11-17 15:39:25,483 INFO  [root] SE.MaxPrecursorMass = 5000
2021-11-17 15:39:25,483 INFO  [root] 
2021-11-17 15:39:25,483 INFO  [root] 
2021-11-17 15:39:25,483 INFO  [root] #Isolation window setting
2021-11-17 15:39:25,483 INFO  [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2021-11-17 15:39:25,483 INFO  [root] WindowType = SWATH
2021-11-17 15:39:25,484 INFO  [root] 
2021-11-17 15:39:25,484 INFO  [root] #Fix window size (For SWATH)
2021-11-17 15:39:25,484 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:39:25,484 INFO  [root] WindowSize = 10
2021-11-17 15:39:25,484 INFO  [root] 
2021-11-17 15:39:25,484 INFO  [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2021-11-17 15:39:25,484 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:39:25,484 INFO  [root] ==window setting begin
2021-11-17 15:39:25,485 INFO  [root] 
2021-11-17 15:39:25,485 INFO  [root] =================================================================================================
2021-11-17 15:39:25,486 INFO  [root] Processing C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.mzXML....
2021-11-17 15:39:25,497 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_diasetting.ser...
2021-11-17 15:39:25,519 INFO  [root] Writing parameter to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_params.ser...
2021-11-17 15:39:25,523 INFO  [root] Module A: Signal extraction
2021-11-17 15:39:28,691 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_diasetting.ser...
2021-11-17 15:39:29,190 INFO  [root] Processing MS1 peak detection
2021-11-17 15:39:29,191 INFO  [root] MS1 average cycle time : 2.6789324 seconds
2021-11-17 15:39:32,609 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:32,609 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:36,733 INFO  [root] 399615 Peak curves found (Memory usage:285MB)
2021-11-17 15:39:36,733 INFO  [root] Inclusion mz values found: 0/0
2021-11-17 15:39:36,733 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:36,735 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:48,847 INFO  [root] No of ion clusters:28130 (Memory usage:228MB)
2021-11-17 15:39:48,872 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_PeakCluster.serFS...
2021-11-17 15:39:49,199 INFO  [root] ==================================================================================
2021-11-17 15:39:49,199 INFO  [root] Processing DIA MS2 (mz range):977.0_980.0( 1/61 )
2021-11-17 15:39:49,275 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:49,275 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:50,137 INFO  [root] 41854 Peak curves found (Memory usage:260MB)
2021-11-17 15:39:50,143 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:50,143 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:50,515 INFO  [root] No of ion clusters:18 (Memory usage:263MB)
2021-11-17 15:39:50,515 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_977_980_PeakCluster.serFS...
2021-11-17 15:39:50,517 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:51,244 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:51,914 INFO  [root] ==================================================================================
2021-11-17 15:39:51,914 INFO  [root] Processing DIA MS2 (mz range):974.0_977.0( 2/61 )
2021-11-17 15:39:51,993 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:51,993 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:52,810 INFO  [root] 50768 Peak curves found (Memory usage:252MB)
2021-11-17 15:39:52,813 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:52,813 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:53,188 INFO  [root] No of ion clusters:5 (Memory usage:256MB)
2021-11-17 15:39:53,188 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_974_977_PeakCluster.serFS...
2021-11-17 15:39:53,189 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:53,432 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:53,790 INFO  [root] ==================================================================================
2021-11-17 15:39:53,790 INFO  [root] Processing DIA MS2 (mz range):971.0_974.0( 3/61 )
2021-11-17 15:39:53,841 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:53,841 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:54,633 INFO  [root] 91201 Peak curves found (Memory usage:269MB)
2021-11-17 15:39:54,636 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:54,636 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:55,062 INFO  [root] No of ion clusters:6 (Memory usage:275MB)
2021-11-17 15:39:55,062 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_971_974_PeakCluster.serFS...
2021-11-17 15:39:55,063 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:55,287 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:55,609 INFO  [root] ==================================================================================
2021-11-17 15:39:55,609 INFO  [root] Processing DIA MS2 (mz range):968.0_971.0( 4/61 )
2021-11-17 15:39:55,648 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:55,649 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:56,128 INFO  [root] 87050 Peak curves found (Memory usage:266MB)
2021-11-17 15:39:56,131 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:56,131 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:56,652 INFO  [root] No of ion clusters:12 (Memory usage:272MB)
2021-11-17 15:39:56,652 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_968_971_PeakCluster.serFS...
2021-11-17 15:39:56,653 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:56,814 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:57,194 INFO  [root] ==================================================================================
2021-11-17 15:39:57,194 INFO  [root] Processing DIA MS2 (mz range):965.0_968.0( 5/61 )
2021-11-17 15:39:57,239 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:57,239 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:57,853 INFO  [root] 93977 Peak curves found (Memory usage:269MB)
2021-11-17 15:39:57,856 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:57,856 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:39:58,331 INFO  [root] No of ion clusters:6 (Memory usage:277MB)
2021-11-17 15:39:58,331 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_965_968_PeakCluster.serFS...
2021-11-17 15:39:58,332 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:39:58,565 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:39:58,882 INFO  [root] ==================================================================================
2021-11-17 15:39:58,882 INFO  [root] Processing DIA MS2 (mz range):962.0_965.0( 6/61 )
2021-11-17 15:39:58,922 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:39:58,922 INFO  [root] Smoothing detected signals......
2021-11-17 15:39:59,662 INFO  [root] 119081 Peak curves found (Memory usage:282MB)
2021-11-17 15:39:59,666 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:39:59,666 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:00,186 INFO  [root] No of ion clusters:15 (Memory usage:291MB)
2021-11-17 15:40:00,186 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_962_965_PeakCluster.serFS...
2021-11-17 15:40:00,187 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:00,589 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:00,946 INFO  [root] ==================================================================================
2021-11-17 15:40:00,946 INFO  [root] Processing DIA MS2 (mz range):959.0_962.0( 7/61 )
2021-11-17 15:40:00,993 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:00,993 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:01,674 INFO  [root] 122236 Peak curves found (Memory usage:285MB)
2021-11-17 15:40:01,676 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:01,676 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:02,170 INFO  [root] No of ion clusters:9 (Memory usage:294MB)
2021-11-17 15:40:02,170 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_959_962_PeakCluster.serFS...
2021-11-17 15:40:02,171 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:02,441 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:02,776 INFO  [root] ==================================================================================
2021-11-17 15:40:02,776 INFO  [root] Processing DIA MS2 (mz range):956.0_959.0( 8/61 )
2021-11-17 15:40:02,813 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:02,813 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:03,438 INFO  [root] 112983 Peak curves found (Memory usage:282MB)
2021-11-17 15:40:03,441 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:03,441 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:03,968 INFO  [root] No of ion clusters:6 (Memory usage:290MB)
2021-11-17 15:40:03,968 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_956_959_PeakCluster.serFS...
2021-11-17 15:40:03,969 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:04,147 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:04,496 INFO  [root] ==================================================================================
2021-11-17 15:40:04,496 INFO  [root] Processing DIA MS2 (mz range):953.0_956.0( 9/61 )
2021-11-17 15:40:04,549 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:04,549 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:05,638 INFO  [root] 102811 Peak curves found (Memory usage:280MB)
2021-11-17 15:40:05,641 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:05,641 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:06,175 INFO  [root] No of ion clusters:18 (Memory usage:288MB)
2021-11-17 15:40:06,175 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_953_956_PeakCluster.serFS...
2021-11-17 15:40:06,176 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:06,414 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:06,768 INFO  [root] ==================================================================================
2021-11-17 15:40:06,768 INFO  [root] Processing DIA MS2 (mz range):950.0_953.0( 10/61 )
2021-11-17 15:40:06,809 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:06,809 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:07,656 INFO  [root] 117261 Peak curves found (Memory usage:286MB)
2021-11-17 15:40:07,658 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:07,658 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:08,188 INFO  [root] No of ion clusters:14 (Memory usage:295MB)
2021-11-17 15:40:08,188 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_950_953_PeakCluster.serFS...
2021-11-17 15:40:08,189 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:08,413 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:08,783 INFO  [root] ==================================================================================
2021-11-17 15:40:08,783 INFO  [root] Processing DIA MS2 (mz range):947.0_950.0( 11/61 )
2021-11-17 15:40:08,825 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:08,825 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:09,438 INFO  [root] 102477 Peak curves found (Memory usage:281MB)
2021-11-17 15:40:09,440 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:09,440 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:09,967 INFO  [root] No of ion clusters:26 (Memory usage:289MB)
2021-11-17 15:40:09,967 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_947_950_PeakCluster.serFS...
2021-11-17 15:40:09,968 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:10,191 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:10,544 INFO  [root] ==================================================================================
2021-11-17 15:40:10,544 INFO  [root] Processing DIA MS2 (mz range):944.0_947.0( 12/61 )
2021-11-17 15:40:10,582 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:10,582 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:11,115 INFO  [root] 99792 Peak curves found (Memory usage:280MB)
2021-11-17 15:40:11,118 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:11,118 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:11,587 INFO  [root] No of ion clusters:16 (Memory usage:288MB)
2021-11-17 15:40:11,588 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_944_947_PeakCluster.serFS...
2021-11-17 15:40:11,588 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:11,783 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:12,113 INFO  [root] ==================================================================================
2021-11-17 15:40:12,113 INFO  [root] Processing DIA MS2 (mz range):941.0_944.0( 13/61 )
2021-11-17 15:40:12,146 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:12,146 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:12,716 INFO  [root] 97741 Peak curves found (Memory usage:281MB)
2021-11-17 15:40:12,718 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:12,718 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:13,195 INFO  [root] No of ion clusters:12 (Memory usage:288MB)
2021-11-17 15:40:13,195 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_941_944_PeakCluster.serFS...
2021-11-17 15:40:13,196 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:13,379 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:13,722 INFO  [root] ==================================================================================
2021-11-17 15:40:13,722 INFO  [root] Processing DIA MS2 (mz range):938.0_941.0( 14/61 )
2021-11-17 15:40:13,771 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:13,771 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:14,435 INFO  [root] 102010 Peak curves found (Memory usage:283MB)
2021-11-17 15:40:14,437 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:14,437 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:14,916 INFO  [root] No of ion clusters:11 (Memory usage:291MB)
2021-11-17 15:40:14,916 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_938_941_PeakCluster.serFS...
2021-11-17 15:40:14,917 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:15,073 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:15,399 INFO  [root] ==================================================================================
2021-11-17 15:40:15,399 INFO  [root] Processing DIA MS2 (mz range):935.0_938.0( 15/61 )
2021-11-17 15:40:15,432 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:15,432 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:16,070 INFO  [root] 96742 Peak curves found (Memory usage:282MB)
2021-11-17 15:40:16,073 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:16,073 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:16,555 INFO  [root] No of ion clusters:8 (Memory usage:289MB)
2021-11-17 15:40:16,555 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_935_938_PeakCluster.serFS...
2021-11-17 15:40:16,556 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:16,729 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:17,070 INFO  [root] ==================================================================================
2021-11-17 15:40:17,070 INFO  [root] Processing DIA MS2 (mz range):932.0_935.0( 16/61 )
2021-11-17 15:40:17,099 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:17,100 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:17,646 INFO  [root] 86561 Peak curves found (Memory usage:278MB)
2021-11-17 15:40:17,648 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:17,648 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:18,093 INFO  [root] No of ion clusters:12 (Memory usage:284MB)
2021-11-17 15:40:18,094 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_932_935_PeakCluster.serFS...
2021-11-17 15:40:18,095 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:18,271 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:18,626 INFO  [root] ==================================================================================
2021-11-17 15:40:18,626 INFO  [root] Processing DIA MS2 (mz range):929.0_932.0( 17/61 )
2021-11-17 15:40:18,657 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:18,657 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:19,229 INFO  [root] 83695 Peak curves found (Memory usage:277MB)
2021-11-17 15:40:19,231 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:19,231 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:19,645 INFO  [root] No of ion clusters:9 (Memory usage:283MB)
2021-11-17 15:40:19,645 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_929_932_PeakCluster.serFS...
2021-11-17 15:40:19,646 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:19,784 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:20,109 INFO  [root] ==================================================================================
2021-11-17 15:40:20,109 INFO  [root] Processing DIA MS2 (mz range):926.0_929.0( 18/61 )
2021-11-17 15:40:20,139 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:20,139 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:20,580 INFO  [root] 81104 Peak curves found (Memory usage:276MB)
2021-11-17 15:40:20,582 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:20,582 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:21,010 INFO  [root] No of ion clusters:11 (Memory usage:283MB)
2021-11-17 15:40:21,010 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_926_929_PeakCluster.serFS...
2021-11-17 15:40:21,011 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:21,146 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:21,508 INFO  [root] ==================================================================================
2021-11-17 15:40:21,508 INFO  [root] Processing DIA MS2 (mz range):923.0_926.0( 19/61 )
2021-11-17 15:40:21,537 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:21,537 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:21,967 INFO  [root] 80872 Peak curves found (Memory usage:277MB)
2021-11-17 15:40:21,968 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:21,968 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:22,385 INFO  [root] No of ion clusters:14 (Memory usage:283MB)
2021-11-17 15:40:22,385 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_923_926_PeakCluster.serFS...
2021-11-17 15:40:22,386 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:22,507 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:22,820 INFO  [root] ==================================================================================
2021-11-17 15:40:22,820 INFO  [root] Processing DIA MS2 (mz range):920.0_923.0( 20/61 )
2021-11-17 15:40:22,848 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:22,849 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:23,267 INFO  [root] 83723 Peak curves found (Memory usage:278MB)
2021-11-17 15:40:23,268 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:23,268 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:23,685 INFO  [root] No of ion clusters:11 (Memory usage:285MB)
2021-11-17 15:40:23,685 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_920_923_PeakCluster.serFS...
2021-11-17 15:40:23,686 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:23,802 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:24,094 INFO  [root] ==================================================================================
2021-11-17 15:40:24,094 INFO  [root] Processing DIA MS2 (mz range):917.0_920.0( 21/61 )
2021-11-17 15:40:24,125 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:24,125 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:24,590 INFO  [root] 79115 Peak curves found (Memory usage:277MB)
2021-11-17 15:40:24,592 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:24,592 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:24,983 INFO  [root] No of ion clusters:12 (Memory usage:283MB)
2021-11-17 15:40:24,983 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_917_920_PeakCluster.serFS...
2021-11-17 15:40:24,984 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:25,103 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:25,446 INFO  [root] ==================================================================================
2021-11-17 15:40:25,446 INFO  [root] Processing DIA MS2 (mz range):914.0_917.0( 22/61 )
2021-11-17 15:40:25,474 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:25,474 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:25,869 INFO  [root] 80010 Peak curves found (Memory usage:277MB)
2021-11-17 15:40:25,870 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:25,870 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:26,248 INFO  [root] No of ion clusters:13 (Memory usage:283MB)
2021-11-17 15:40:26,248 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_914_917_PeakCluster.serFS...
2021-11-17 15:40:26,249 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:26,337 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:26,623 INFO  [root] ==================================================================================
2021-11-17 15:40:26,623 INFO  [root] Processing DIA MS2 (mz range):911.0_914.0( 23/61 )
2021-11-17 15:40:26,650 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:26,650 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:27,068 INFO  [root] 80897 Peak curves found (Memory usage:279MB)
2021-11-17 15:40:27,070 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:27,070 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:27,460 INFO  [root] No of ion clusters:10 (Memory usage:285MB)
2021-11-17 15:40:27,460 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_911_914_PeakCluster.serFS...
2021-11-17 15:40:27,460 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:27,585 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:27,939 INFO  [root] ==================================================================================
2021-11-17 15:40:27,939 INFO  [root] Processing DIA MS2 (mz range):908.0_911.0( 24/61 )
2021-11-17 15:40:27,967 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:27,967 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:28,383 INFO  [root] 80598 Peak curves found (Memory usage:279MB)
2021-11-17 15:40:28,386 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:28,386 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:28,771 INFO  [root] No of ion clusters:21 (Memory usage:285MB)
2021-11-17 15:40:28,772 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_908_911_PeakCluster.serFS...
2021-11-17 15:40:28,772 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:28,963 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:29,314 INFO  [root] ==================================================================================
2021-11-17 15:40:29,314 INFO  [root] Processing DIA MS2 (mz range):905.0_908.0( 25/61 )
2021-11-17 15:40:29,343 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:29,343 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:29,819 INFO  [root] 92280 Peak curves found (Memory usage:284MB)
2021-11-17 15:40:29,822 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:29,822 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:30,289 INFO  [root] No of ion clusters:15 (Memory usage:291MB)
2021-11-17 15:40:30,289 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_905_908_PeakCluster.serFS...
2021-11-17 15:40:30,290 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:30,436 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:30,746 INFO  [root] ==================================================================================
2021-11-17 15:40:30,746 INFO  [root] Processing DIA MS2 (mz range):902.0_905.0( 26/61 )
2021-11-17 15:40:30,777 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:30,777 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:31,442 INFO  [root] 89339 Peak curves found (Memory usage:284MB)
2021-11-17 15:40:31,443 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:31,443 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:31,898 INFO  [root] No of ion clusters:10 (Memory usage:291MB)
2021-11-17 15:40:31,898 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_902_905_PeakCluster.serFS...
2021-11-17 15:40:31,899 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:32,038 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:32,337 INFO  [root] ==================================================================================
2021-11-17 15:40:32,337 INFO  [root] Processing DIA MS2 (mz range):899.0_902.0( 27/61 )
2021-11-17 15:40:32,374 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:32,374 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:32,895 INFO  [root] 97424 Peak curves found (Memory usage:287MB)
2021-11-17 15:40:32,897 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:32,897 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:33,206 INFO  [root] No of ion clusters:7 (Memory usage:292MB)
2021-11-17 15:40:33,206 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_899_902_PeakCluster.serFS...
2021-11-17 15:40:33,208 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:33,313 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:33,613 INFO  [root] ==================================================================================
2021-11-17 15:40:33,613 INFO  [root] Processing DIA MS2 (mz range):896.0_899.0( 28/61 )
2021-11-17 15:40:33,651 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:33,651 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:34,626 INFO  [root] 97030 Peak curves found (Memory usage:286MB)
2021-11-17 15:40:34,628 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:34,628 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:35,055 INFO  [root] No of ion clusters:11 (Memory usage:293MB)
2021-11-17 15:40:35,055 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_896_899_PeakCluster.serFS...
2021-11-17 15:40:35,056 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:35,215 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:35,509 INFO  [root] ==================================================================================
2021-11-17 15:40:35,510 INFO  [root] Processing DIA MS2 (mz range):893.0_896.0( 29/61 )
2021-11-17 15:40:35,554 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:35,554 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:36,156 INFO  [root] 114252 Peak curves found (Memory usage:293MB)
2021-11-17 15:40:36,157 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:36,157 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:36,626 INFO  [root] No of ion clusters:13 (Memory usage:302MB)
2021-11-17 15:40:36,626 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_893_896_PeakCluster.serFS...
2021-11-17 15:40:36,626 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:36,814 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:37,155 INFO  [root] ==================================================================================
2021-11-17 15:40:37,155 INFO  [root] Processing DIA MS2 (mz range):890.0_893.0( 30/61 )
2021-11-17 15:40:37,211 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:37,211 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:37,715 INFO  [root] 97070 Peak curves found (Memory usage:286MB)
2021-11-17 15:40:37,717 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:37,717 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:38,140 INFO  [root] No of ion clusters:6 (Memory usage:294MB)
2021-11-17 15:40:38,140 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_890_893_PeakCluster.serFS...
2021-11-17 15:40:38,140 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:38,243 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:38,543 INFO  [root] ==================================================================================
2021-11-17 15:40:38,543 INFO  [root] Processing DIA MS2 (mz range):887.0_890.0( 31/61 )
2021-11-17 15:40:38,571 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:38,572 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:39,000 INFO  [root] 78115 Peak curves found (Memory usage:280MB)
2021-11-17 15:40:39,001 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:39,002 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:39,394 INFO  [root] No of ion clusters:15 (Memory usage:286MB)
2021-11-17 15:40:39,394 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_887_890_PeakCluster.serFS...
2021-11-17 15:40:39,395 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:39,497 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:39,795 INFO  [root] ==================================================================================
2021-11-17 15:40:39,795 INFO  [root] Processing DIA MS2 (mz range):884.0_887.0( 32/61 )
2021-11-17 15:40:39,823 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:39,823 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:40,231 INFO  [root] 82365 Peak curves found (Memory usage:282MB)
2021-11-17 15:40:40,233 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:40,233 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:40,614 INFO  [root] No of ion clusters:6 (Memory usage:288MB)
2021-11-17 15:40:40,614 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_884_887_PeakCluster.serFS...
2021-11-17 15:40:40,615 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:40,721 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:41,016 INFO  [root] ==================================================================================
2021-11-17 15:40:41,016 INFO  [root] Processing DIA MS2 (mz range):881.0_884.0( 33/61 )
2021-11-17 15:40:41,051 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:41,051 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:41,451 INFO  [root] 77150 Peak curves found (Memory usage:280MB)
2021-11-17 15:40:41,453 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:41,453 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:41,850 INFO  [root] No of ion clusters:9 (Memory usage:286MB)
2021-11-17 15:40:41,850 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_881_884_PeakCluster.serFS...
2021-11-17 15:40:41,851 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:41,960 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:42,290 INFO  [root] ==================================================================================
2021-11-17 15:40:42,290 INFO  [root] Processing DIA MS2 (mz range):878.0_881.0( 34/61 )
2021-11-17 15:40:42,319 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:42,319 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:42,742 INFO  [root] 78913 Peak curves found (Memory usage:281MB)
2021-11-17 15:40:42,744 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:42,744 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:43,148 INFO  [root] No of ion clusters:7 (Memory usage:287MB)
2021-11-17 15:40:43,148 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_878_881_PeakCluster.serFS...
2021-11-17 15:40:43,149 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:43,251 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:43,539 INFO  [root] ==================================================================================
2021-11-17 15:40:43,539 INFO  [root] Processing DIA MS2 (mz range):875.0_878.0( 35/61 )
2021-11-17 15:40:43,573 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:43,573 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:44,023 INFO  [root] 89949 Peak curves found (Memory usage:286MB)
2021-11-17 15:40:44,024 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:44,024 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:44,447 INFO  [root] No of ion clusters:9 (Memory usage:293MB)
2021-11-17 15:40:44,447 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_875_878_PeakCluster.serFS...
2021-11-17 15:40:44,448 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:44,596 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:44,885 INFO  [root] ==================================================================================
2021-11-17 15:40:44,885 INFO  [root] Processing DIA MS2 (mz range):872.0_875.0( 36/61 )
2021-11-17 15:40:44,921 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:44,921 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:45,541 INFO  [root] 96638 Peak curves found (Memory usage:290MB)
2021-11-17 15:40:45,542 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:45,542 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:46,000 INFO  [root] No of ion clusters:6 (Memory usage:298MB)
2021-11-17 15:40:46,001 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_872_875_PeakCluster.serFS...
2021-11-17 15:40:46,001 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:46,179 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:46,487 INFO  [root] ==================================================================================
2021-11-17 15:40:46,487 INFO  [root] Processing DIA MS2 (mz range):869.0_872.0( 37/61 )
2021-11-17 15:40:46,519 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:46,519 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:47,027 INFO  [root] 94393 Peak curves found (Memory usage:289MB)
2021-11-17 15:40:47,029 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:47,029 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:47,453 INFO  [root] No of ion clusters:8 (Memory usage:296MB)
2021-11-17 15:40:47,454 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_869_872_PeakCluster.serFS...
2021-11-17 15:40:47,454 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:47,598 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:47,896 INFO  [root] ==================================================================================
2021-11-17 15:40:47,896 INFO  [root] Processing DIA MS2 (mz range):866.0_869.0( 38/61 )
2021-11-17 15:40:47,927 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:47,927 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:48,340 INFO  [root] 87272 Peak curves found (Memory usage:286MB)
2021-11-17 15:40:48,342 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:48,342 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:48,745 INFO  [root] No of ion clusters:6 (Memory usage:293MB)
2021-11-17 15:40:48,745 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_866_869_PeakCluster.serFS...
2021-11-17 15:40:48,746 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:48,889 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:49,212 INFO  [root] ==================================================================================
2021-11-17 15:40:49,212 INFO  [root] Processing DIA MS2 (mz range):863.0_866.0( 39/61 )
2021-11-17 15:40:49,245 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:49,245 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:49,714 INFO  [root] 86989 Peak curves found (Memory usage:287MB)
2021-11-17 15:40:49,716 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:49,716 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:50,115 INFO  [root] No of ion clusters:19 (Memory usage:293MB)
2021-11-17 15:40:50,115 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_863_866_PeakCluster.serFS...
2021-11-17 15:40:50,116 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:50,288 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:50,597 INFO  [root] ==================================================================================
2021-11-17 15:40:50,597 INFO  [root] Processing DIA MS2 (mz range):860.0_863.0( 40/61 )
2021-11-17 15:40:50,628 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:50,628 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:51,092 INFO  [root] 92486 Peak curves found (Memory usage:290MB)
2021-11-17 15:40:51,093 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:51,093 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:51,508 INFO  [root] No of ion clusters:10 (Memory usage:296MB)
2021-11-17 15:40:51,508 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_860_863_PeakCluster.serFS...
2021-11-17 15:40:51,509 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:51,670 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:51,977 INFO  [root] ==================================================================================
2021-11-17 15:40:51,977 INFO  [root] Processing DIA MS2 (mz range):857.0_860.0( 41/61 )
2021-11-17 15:40:52,009 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:52,009 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:52,502 INFO  [root] 102306 Peak curves found (Memory usage:294MB)
2021-11-17 15:40:52,504 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:52,504 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:52,956 INFO  [root] No of ion clusters:7 (Memory usage:302MB)
2021-11-17 15:40:52,957 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_857_860_PeakCluster.serFS...
2021-11-17 15:40:52,957 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:53,124 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:53,427 INFO  [root] ==================================================================================
2021-11-17 15:40:53,427 INFO  [root] Processing DIA MS2 (mz range):854.0_857.0( 42/61 )
2021-11-17 15:40:53,463 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:53,463 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:54,325 INFO  [root] 94450 Peak curves found (Memory usage:292MB)
2021-11-17 15:40:54,328 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:54,328 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:54,784 INFO  [root] No of ion clusters:9 (Memory usage:299MB)
2021-11-17 15:40:54,784 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_854_857_PeakCluster.serFS...
2021-11-17 15:40:54,785 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:54,994 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:55,340 INFO  [root] ==================================================================================
2021-11-17 15:40:55,340 INFO  [root] Processing DIA MS2 (mz range):851.0_854.0( 43/61 )
2021-11-17 15:40:55,372 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:55,372 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:55,912 INFO  [root] 106545 Peak curves found (Memory usage:296MB)
2021-11-17 15:40:55,914 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:55,914 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:56,410 INFO  [root] No of ion clusters:11 (Memory usage:303MB)
2021-11-17 15:40:56,410 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_851_854_PeakCluster.serFS...
2021-11-17 15:40:56,411 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:56,563 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:56,875 INFO  [root] ==================================================================================
2021-11-17 15:40:56,875 INFO  [root] Processing DIA MS2 (mz range):848.0_851.0( 44/61 )
2021-11-17 15:40:56,908 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:56,908 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:57,441 INFO  [root] 95582 Peak curves found (Memory usage:292MB)
2021-11-17 15:40:57,444 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:57,444 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:57,857 INFO  [root] No of ion clusters:8 (Memory usage:299MB)
2021-11-17 15:40:57,857 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_848_851_PeakCluster.serFS...
2021-11-17 15:40:57,858 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:58,031 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:58,342 INFO  [root] ==================================================================================
2021-11-17 15:40:58,342 INFO  [root] Processing DIA MS2 (mz range):845.0_848.0( 45/61 )
2021-11-17 15:40:58,377 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:58,377 INFO  [root] Smoothing detected signals......
2021-11-17 15:40:58,892 INFO  [root] 95961 Peak curves found (Memory usage:292MB)
2021-11-17 15:40:58,894 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:40:58,894 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:40:59,322 INFO  [root] No of ion clusters:8 (Memory usage:299MB)
2021-11-17 15:40:59,322 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_845_848_PeakCluster.serFS...
2021-11-17 15:40:59,323 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:40:59,553 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:40:59,889 INFO  [root] ==================================================================================
2021-11-17 15:40:59,889 INFO  [root] Processing DIA MS2 (mz range):842.0_845.0( 46/61 )
2021-11-17 15:40:59,921 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:40:59,921 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:00,481 INFO  [root] 93228 Peak curves found (Memory usage:291MB)
2021-11-17 15:41:00,483 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:00,483 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:00,924 INFO  [root] No of ion clusters:12 (Memory usage:298MB)
2021-11-17 15:41:00,924 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_842_845_PeakCluster.serFS...
2021-11-17 15:41:00,925 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:01,100 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:01,421 INFO  [root] ==================================================================================
2021-11-17 15:41:01,421 INFO  [root] Processing DIA MS2 (mz range):839.0_842.0( 47/61 )
2021-11-17 15:41:01,455 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:01,455 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:01,999 INFO  [root] 96980 Peak curves found (Memory usage:294MB)
2021-11-17 15:41:02,001 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:02,001 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:02,440 INFO  [root] No of ion clusters:6 (Memory usage:301MB)
2021-11-17 15:41:02,440 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_839_842_PeakCluster.serFS...
2021-11-17 15:41:02,441 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:02,704 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:03,054 INFO  [root] ==================================================================================
2021-11-17 15:41:03,054 INFO  [root] Processing DIA MS2 (mz range):836.0_839.0( 48/61 )
2021-11-17 15:41:03,093 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:03,094 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:03,667 INFO  [root] 101630 Peak curves found (Memory usage:296MB)
2021-11-17 15:41:03,668 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:03,668 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:04,105 INFO  [root] No of ion clusters:13 (Memory usage:303MB)
2021-11-17 15:41:04,105 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_836_839_PeakCluster.serFS...
2021-11-17 15:41:04,106 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:04,322 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:04,638 INFO  [root] ==================================================================================
2021-11-17 15:41:04,638 INFO  [root] Processing DIA MS2 (mz range):833.0_836.0( 49/61 )
2021-11-17 15:41:04,670 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:04,670 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:05,167 INFO  [root] 107277 Peak curves found (Memory usage:298MB)
2021-11-17 15:41:05,169 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:05,169 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:05,613 INFO  [root] No of ion clusters:7 (Memory usage:306MB)
2021-11-17 15:41:05,613 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_833_836_PeakCluster.serFS...
2021-11-17 15:41:05,614 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:05,774 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:06,088 INFO  [root] ==================================================================================
2021-11-17 15:41:06,088 INFO  [root] Processing DIA MS2 (mz range):830.0_833.0( 50/61 )
2021-11-17 15:41:06,128 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:06,128 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:06,717 INFO  [root] 104715 Peak curves found (Memory usage:297MB)
2021-11-17 15:41:06,719 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:06,719 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:07,158 INFO  [root] No of ion clusters:7 (Memory usage:305MB)
2021-11-17 15:41:07,158 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_830_833_PeakCluster.serFS...
2021-11-17 15:41:07,159 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:07,438 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:07,751 INFO  [root] ==================================================================================
2021-11-17 15:41:07,751 INFO  [root] Processing DIA MS2 (mz range):827.0_830.0( 51/61 )
2021-11-17 15:41:07,785 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:07,785 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:08,334 INFO  [root] 110806 Peak curves found (Memory usage:300MB)
2021-11-17 15:41:08,335 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:08,336 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:08,793 INFO  [root] No of ion clusters:10 (Memory usage:308MB)
2021-11-17 15:41:08,793 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_827_830_PeakCluster.serFS...
2021-11-17 15:41:08,794 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:08,980 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:09,329 INFO  [root] ==================================================================================
2021-11-17 15:41:09,329 INFO  [root] Processing DIA MS2 (mz range):824.0_827.0( 52/61 )
2021-11-17 15:41:09,373 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:09,373 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:09,896 INFO  [root] 109507 Peak curves found (Memory usage:299MB)
2021-11-17 15:41:09,897 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:09,897 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:10,350 INFO  [root] No of ion clusters:11 (Memory usage:308MB)
2021-11-17 15:41:10,350 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_824_827_PeakCluster.serFS...
2021-11-17 15:41:10,351 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:10,559 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:10,890 INFO  [root] ==================================================================================
2021-11-17 15:41:10,890 INFO  [root] Processing DIA MS2 (mz range):821.0_824.0( 53/61 )
2021-11-17 15:41:10,929 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:10,929 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:11,625 INFO  [root] 126745 Peak curves found (Memory usage:306MB)
2021-11-17 15:41:11,627 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:11,627 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:12,110 INFO  [root] No of ion clusters:9 (Memory usage:316MB)
2021-11-17 15:41:12,110 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_821_824_PeakCluster.serFS...
2021-11-17 15:41:12,111 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:12,341 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:12,669 INFO  [root] ==================================================================================
2021-11-17 15:41:12,669 INFO  [root] Processing DIA MS2 (mz range):818.0_821.0( 54/61 )
2021-11-17 15:41:12,716 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:12,716 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:13,480 INFO  [root] 127676 Peak curves found (Memory usage:307MB)
2021-11-17 15:41:13,482 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:13,482 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:13,956 INFO  [root] No of ion clusters:13 (Memory usage:317MB)
2021-11-17 15:41:13,956 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_818_821_PeakCluster.serFS...
2021-11-17 15:41:13,957 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:14,295 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:14,722 INFO  [root] ==================================================================================
2021-11-17 15:41:14,722 INFO  [root] Processing DIA MS2 (mz range):815.0_818.0( 55/61 )
2021-11-17 15:41:14,758 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:14,758 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:15,310 INFO  [root] 115008 Peak curves found (Memory usage:302MB)
2021-11-17 15:41:15,311 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:15,311 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:15,816 INFO  [root] No of ion clusters:11 (Memory usage:310MB)
2021-11-17 15:41:15,816 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_815_818_PeakCluster.serFS...
2021-11-17 15:41:15,818 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:16,018 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:16,348 INFO  [root] ==================================================================================
2021-11-17 15:41:16,348 INFO  [root] Processing DIA MS2 (mz range):812.0_815.0( 56/61 )
2021-11-17 15:41:16,385 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:16,385 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:17,094 INFO  [root] 103893 Peak curves found (Memory usage:298MB)
2021-11-17 15:41:17,096 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:17,096 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:17,531 INFO  [root] No of ion clusters:8 (Memory usage:306MB)
2021-11-17 15:41:17,531 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_812_815_PeakCluster.serFS...
2021-11-17 15:41:17,532 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:17,747 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:18,060 INFO  [root] ==================================================================================
2021-11-17 15:41:18,060 INFO  [root] Processing DIA MS2 (mz range):809.0_812.0( 57/61 )
2021-11-17 15:41:18,095 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:18,095 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:18,625 INFO  [root] 102634 Peak curves found (Memory usage:297MB)
2021-11-17 15:41:18,627 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:18,627 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:19,068 INFO  [root] No of ion clusters:12 (Memory usage:305MB)
2021-11-17 15:41:19,068 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_809_812_PeakCluster.serFS...
2021-11-17 15:41:19,069 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:19,346 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:19,676 INFO  [root] ==================================================================================
2021-11-17 15:41:19,676 INFO  [root] Processing DIA MS2 (mz range):806.0_809.0( 58/61 )
2021-11-17 15:41:19,710 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:19,710 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:20,302 INFO  [root] 103973 Peak curves found (Memory usage:299MB)
2021-11-17 15:41:20,304 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:20,304 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:20,749 INFO  [root] No of ion clusters:12 (Memory usage:307MB)
2021-11-17 15:41:20,749 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_806_809_PeakCluster.serFS...
2021-11-17 15:41:20,750 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:20,960 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:21,290 INFO  [root] ==================================================================================
2021-11-17 15:41:21,290 INFO  [root] Processing DIA MS2 (mz range):803.0_806.0( 59/61 )
2021-11-17 15:41:21,334 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:21,334 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:22,055 INFO  [root] 115075 Peak curves found (Memory usage:304MB)
2021-11-17 15:41:22,056 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:22,056 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:22,517 INFO  [root] No of ion clusters:7 (Memory usage:312MB)
2021-11-17 15:41:22,517 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_803_806_PeakCluster.serFS...
2021-11-17 15:41:22,517 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:22,776 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:23,119 INFO  [root] ==================================================================================
2021-11-17 15:41:23,119 INFO  [root] Processing DIA MS2 (mz range):800.0_803.0( 60/61 )
2021-11-17 15:41:23,148 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:23,148 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:23,692 INFO  [root] 69401 Peak curves found (Memory usage:285MB)
2021-11-17 15:41:23,694 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:23,694 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:24,148 INFO  [root] No of ion clusters:14 (Memory usage:291MB)
2021-11-17 15:41:24,148 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_800_803_PeakCluster.serFS...
2021-11-17 15:41:24,149 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:24,357 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:24,697 INFO  [root] ==================================================================================
2021-11-17 15:41:24,697 INFO  [root] Processing DIA MS2 (mz range):797.0_800.0( 61/61 )
2021-11-17 15:41:24,719 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:24,719 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:25,439 INFO  [root] 55617 Peak curves found (Memory usage:284MB)
2021-11-17 15:41:25,441 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:25,441 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:25,790 INFO  [root] No of ion clusters:39 (Memory usage:289MB)
2021-11-17 15:41:25,790 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_797_800_PeakCluster.serFS...
2021-11-17 15:41:25,791 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:26,309 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:26,760 INFO  [root] ==================================================================================
Process 'UmpireSe' finished, exit code: 0
2021-11-17 15:41:28,126 INFO  [root] C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.mzXML processed time:0 hour, 2 min, 2 sec
2021-11-17 15:41:28,126 INFO  [root] Job complete
2021-11-17 15:41:28,126 INFO  [root] =================================================================================================
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
=================================================================================================
DIA-Umpire singal extraction analysis  (version: v2.2.3)
(c) University of Michigan
2021-11-17 15:41:35,666 INFO  [root] Version: v2.2.3
2021-11-17 15:41:35,667 INFO  [root] Parameter file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
2021-11-17 15:41:35,667 INFO  [root] Spectra file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.mzXML
2021-11-17 15:41:35,669 INFO  [root] 
2021-11-17 15:41:35,669 INFO  [root] ####################################################################################################
2021-11-17 15:41:35,669 INFO  [root] #No of threads
2021-11-17 15:41:35,669 INFO  [root] Thread = 7
2021-11-17 15:41:35,670 INFO  [root] ####################################################################################################
2021-11-17 15:41:35,670 INFO  [root] 
2021-11-17 15:41:35,670 INFO  [root] ## omit Thread
2021-11-17 15:41:35,670 INFO  [root] 
2021-11-17 15:41:35,670 INFO  [root] #Precursor-fragments grouping parameters
2021-11-17 15:41:35,670 INFO  [root] RPmax = 25
2021-11-17 15:41:35,670 INFO  [root] RFmax = 500
2021-11-17 15:41:35,670 INFO  [root] CorrThreshold = 0
2021-11-17 15:41:35,671 INFO  [root] DeltaApex = 0.2
2021-11-17 15:41:35,671 INFO  [root] RTOverlap = 0.3
2021-11-17 15:41:35,671 INFO  [root] 
2021-11-17 15:41:35,671 INFO  [root] #Fragment intensity adjustments
2021-11-17 15:41:35,671 INFO  [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2021-11-17 15:41:35,671 INFO  [root] AdjustFragIntensity = true
2021-11-17 15:41:35,671 INFO  [root] BoostComplementaryIon = false
2021-11-17 15:41:35,671 INFO  [root] 
2021-11-17 15:41:35,671 INFO  [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2021-11-17 15:41:35,671 INFO  [root] ExportPrecursorPeak = false
2021-11-17 15:41:35,671 INFO  [root] 
2021-11-17 15:41:35,671 INFO  [root] Q1 = true
2021-11-17 15:41:35,671 INFO  [root] Q2 = true
2021-11-17 15:41:35,671 INFO  [root] Q3 = true
2021-11-17 15:41:35,672 INFO  [root] 
2021-11-17 15:41:35,672 INFO  [root] #Signal extraction: mass accuracy and resolution
2021-11-17 15:41:35,672 INFO  [root] # resolution parameter matters only for data generated in profile mode
2021-11-17 15:41:35,672 INFO  [root] SE.MS1PPM = 10
2021-11-17 15:41:35,672 INFO  [root] SE.MS2PPM = 10
2021-11-17 15:41:35,672 INFO  [root] SE.Resolution = 60000
2021-11-17 15:41:35,672 INFO  [root] 
2021-11-17 15:41:35,672 INFO  [root] #Signal extraction: signal to noise filter
2021-11-17 15:41:35,672 INFO  [root] SE.SN = 1.1
2021-11-17 15:41:35,672 INFO  [root] SE.MS2SN = 1.1
2021-11-17 15:41:35,672 INFO  [root] 
2021-11-17 15:41:35,672 INFO  [root] #Signal extraction: minimum signal intensity filter
2021-11-17 15:41:35,672 INFO  [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2021-11-17 15:41:35,672 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2021-11-17 15:41:35,672 INFO  [root] SE.EstimateBG = false
2021-11-17 15:41:35,672 INFO  [root] SE.MinMSIntensity = 1
2021-11-17 15:41:35,673 INFO  [root] SE.MinMSMSIntensity = 1
2021-11-17 15:41:35,673 INFO  [root] 
2021-11-17 15:41:35,673 INFO  [root] #Signal extraction: peak curve detection and isotope grouping
2021-11-17 15:41:35,673 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2021-11-17 15:41:35,673 INFO  [root] SE.NoMissedScan = 1
2021-11-17 15:41:35,673 INFO  [root] SE.MaxCurveRTRange = 2
2021-11-17 15:41:35,673 INFO  [root] SE.RemoveGroupedPeaks = true
2021-11-17 15:41:35,673 INFO  [root] SE.RemoveGroupedPeaksRTOverlap = 0.3
2021-11-17 15:41:35,673 INFO  [root] SE.RemoveGroupedPeaksCorr = 0.3
2021-11-17 15:41:35,673 INFO  [root] SE.MinNoPeakCluster = 2
2021-11-17 15:41:35,674 INFO  [root] SE.MaxNoPeakCluster = 4
2021-11-17 15:41:35,847 INFO  [root] 
2021-11-17 15:41:35,847 INFO  [root] #Signal extraction: filtering of MS1 features
2021-11-17 15:41:35,847 INFO  [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2021-11-17 15:41:35,847 INFO  [root] SE.IsoPattern = 0.3
2021-11-17 15:41:35,847 INFO  [root] SE.MassDefectFilter = false
2021-11-17 15:41:35,847 INFO  [root] SE.MassDefectOffset = 0.1
2021-11-17 15:41:35,847 INFO  [root] 
2021-11-17 15:41:35,848 INFO  [root] #Signal extraction: other
2021-11-17 15:41:35,848 INFO  [root] SE.StartCharge = 1
2021-11-17 15:41:35,848 INFO  [root] SE.EndCharge = 5
2021-11-17 15:41:35,848 INFO  [root] SE.MS2StartCharge = 2
2021-11-17 15:41:35,848 INFO  [root] SE.MS2EndCharge = 5
2021-11-17 15:41:35,848 INFO  [root] SE.MinFrag = 10
2021-11-17 15:41:35,848 INFO  [root] SE.StartRT = 0
2021-11-17 15:41:35,848 INFO  [root] SE.EndRT = 9999
2021-11-17 15:41:35,848 INFO  [root] SE.MinMZ = 200
2021-11-17 15:41:35,848 INFO  [root] SE.MinPrecursorMass = 600
2021-11-17 15:41:35,848 INFO  [root] SE.MaxPrecursorMass = 5000
2021-11-17 15:41:35,848 INFO  [root] 
2021-11-17 15:41:35,849 INFO  [root] 
2021-11-17 15:41:35,849 INFO  [root] #Isolation window setting
2021-11-17 15:41:35,849 INFO  [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2021-11-17 15:41:35,849 INFO  [root] WindowType = SWATH
2021-11-17 15:41:35,849 INFO  [root] 
2021-11-17 15:41:35,849 INFO  [root] #Fix window size (For SWATH)
2021-11-17 15:41:35,849 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:41:35,849 INFO  [root] WindowSize = 10
2021-11-17 15:41:35,849 INFO  [root] 
2021-11-17 15:41:35,849 INFO  [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2021-11-17 15:41:35,849 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:41:35,849 INFO  [root] ==window setting begin
2021-11-17 15:41:35,849 INFO  [root] 
2021-11-17 15:41:35,850 INFO  [root] =================================================================================================
2021-11-17 15:41:35,850 INFO  [root] Processing C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.mzXML....
2021-11-17 15:41:35,855 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_diasetting.ser...
2021-11-17 15:41:35,866 INFO  [root] Writing parameter to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_params.ser...
2021-11-17 15:41:35,868 INFO  [root] Module A: Signal extraction
2021-11-17 15:41:39,618 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_diasetting.ser...
2021-11-17 15:41:40,110 INFO  [root] Processing MS1 peak detection
2021-11-17 15:41:40,111 INFO  [root] MS1 average cycle time : 2.6778212 seconds
2021-11-17 15:41:44,068 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:44,068 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:47,568 INFO  [root] 244553 Peak curves found (Memory usage:249MB)
2021-11-17 15:41:47,568 INFO  [root] Inclusion mz values found: 0/0
2021-11-17 15:41:47,568 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:47,570 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:54,885 INFO  [root] No of ion clusters:21872 (Memory usage:155MB)
2021-11-17 15:41:54,902 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_PeakCluster.serFS...
2021-11-17 15:41:55,138 INFO  [root] ==================================================================================
2021-11-17 15:41:55,138 INFO  [root] Processing DIA MS2 (mz range):977.0_980.0( 1/61 )
2021-11-17 15:41:55,194 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:55,194 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:56,045 INFO  [root] 54960 Peak curves found (Memory usage:194MB)
2021-11-17 15:41:56,049 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:56,049 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:56,311 INFO  [root] No of ion clusters:31 (Memory usage:199MB)
2021-11-17 15:41:56,311 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_977_980_PeakCluster.serFS...
2021-11-17 15:41:56,312 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:56,872 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:57,580 INFO  [root] ==================================================================================
2021-11-17 15:41:57,580 INFO  [root] Processing DIA MS2 (mz range):974.0_977.0( 2/61 )
2021-11-17 15:41:57,637 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:57,637 INFO  [root] Smoothing detected signals......
2021-11-17 15:41:58,646 INFO  [root] 74323 Peak curves found (Memory usage:190MB)
2021-11-17 15:41:58,648 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:41:58,648 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:41:58,944 INFO  [root] No of ion clusters:19 (Memory usage:196MB)
2021-11-17 15:41:58,944 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_974_977_PeakCluster.serFS...
2021-11-17 15:41:58,946 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:41:59,317 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:41:59,622 INFO  [root] ==================================================================================
2021-11-17 15:41:59,623 INFO  [root] Processing DIA MS2 (mz range):971.0_974.0( 3/61 )
2021-11-17 15:41:59,683 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:41:59,683 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:00,961 INFO  [root] 113782 Peak curves found (Memory usage:207MB)
2021-11-17 15:42:00,964 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:00,964 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:01,351 INFO  [root] No of ion clusters:11 (Memory usage:216MB)
2021-11-17 15:42:01,351 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_971_974_PeakCluster.serFS...
2021-11-17 15:42:01,352 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:01,720 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:02,003 INFO  [root] ==================================================================================
2021-11-17 15:42:02,003 INFO  [root] Processing DIA MS2 (mz range):968.0_971.0( 4/61 )
2021-11-17 15:42:02,045 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:02,045 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:02,924 INFO  [root] 100474 Peak curves found (Memory usage:201MB)
2021-11-17 15:42:02,926 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:02,926 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:03,278 INFO  [root] No of ion clusters:15 (Memory usage:209MB)
2021-11-17 15:42:03,278 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_968_971_PeakCluster.serFS...
2021-11-17 15:42:03,279 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:03,598 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:03,836 INFO  [root] ==================================================================================
2021-11-17 15:42:03,836 INFO  [root] Processing DIA MS2 (mz range):965.0_968.0( 5/61 )
2021-11-17 15:42:03,880 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:03,880 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:04,679 INFO  [root] 107405 Peak curves found (Memory usage:203MB)
2021-11-17 15:42:04,683 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:04,683 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:05,019 INFO  [root] No of ion clusters:6 (Memory usage:212MB)
2021-11-17 15:42:05,019 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_965_968_PeakCluster.serFS...
2021-11-17 15:42:05,020 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:05,265 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:05,504 INFO  [root] ==================================================================================
2021-11-17 15:42:05,504 INFO  [root] Processing DIA MS2 (mz range):962.0_965.0( 6/61 )
2021-11-17 15:42:05,546 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:05,547 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:06,493 INFO  [root] 111603 Peak curves found (Memory usage:207MB)
2021-11-17 15:42:06,497 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:06,497 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:06,866 INFO  [root] No of ion clusters:12 (Memory usage:216MB)
2021-11-17 15:42:06,866 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_962_965_PeakCluster.serFS...
2021-11-17 15:42:06,867 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:07,149 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:07,387 INFO  [root] ==================================================================================
2021-11-17 15:42:07,387 INFO  [root] Processing DIA MS2 (mz range):959.0_962.0( 7/61 )
2021-11-17 15:42:07,425 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:07,425 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:08,327 INFO  [root] 111941 Peak curves found (Memory usage:208MB)
2021-11-17 15:42:08,329 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:08,329 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:08,735 INFO  [root] No of ion clusters:13 (Memory usage:216MB)
2021-11-17 15:42:08,735 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_959_962_PeakCluster.serFS...
2021-11-17 15:42:08,746 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:08,933 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:09,157 INFO  [root] ==================================================================================
2021-11-17 15:42:09,157 INFO  [root] Processing DIA MS2 (mz range):956.0_959.0( 8/61 )
2021-11-17 15:42:09,197 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:09,197 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:10,064 INFO  [root] 119437 Peak curves found (Memory usage:211MB)
2021-11-17 15:42:10,065 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:10,065 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:10,448 INFO  [root] No of ion clusters:15 (Memory usage:220MB)
2021-11-17 15:42:10,449 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_956_959_PeakCluster.serFS...
2021-11-17 15:42:10,449 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:10,631 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:10,868 INFO  [root] ==================================================================================
2021-11-17 15:42:10,868 INFO  [root] Processing DIA MS2 (mz range):953.0_956.0( 9/61 )
2021-11-17 15:42:10,917 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:10,917 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:12,810 INFO  [root] 124240 Peak curves found (Memory usage:216MB)
2021-11-17 15:42:12,812 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:12,812 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:13,195 INFO  [root] No of ion clusters:18 (Memory usage:226MB)
2021-11-17 15:42:13,195 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_953_956_PeakCluster.serFS...
2021-11-17 15:42:13,196 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:13,395 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:13,643 INFO  [root] ==================================================================================
2021-11-17 15:42:13,643 INFO  [root] Processing DIA MS2 (mz range):950.0_953.0( 10/61 )
2021-11-17 15:42:13,693 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:13,693 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:14,663 INFO  [root] 132873 Peak curves found (Memory usage:218MB)
2021-11-17 15:42:14,665 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:14,665 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:15,106 INFO  [root] No of ion clusters:14 (Memory usage:229MB)
2021-11-17 15:42:15,106 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_950_953_PeakCluster.serFS...
2021-11-17 15:42:15,107 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:15,342 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:15,584 INFO  [root] ==================================================================================
2021-11-17 15:42:15,584 INFO  [root] Processing DIA MS2 (mz range):947.0_950.0( 11/61 )
2021-11-17 15:42:15,637 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:15,637 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:16,571 INFO  [root] 119028 Peak curves found (Memory usage:214MB)
2021-11-17 15:42:16,573 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:16,573 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:16,982 INFO  [root] No of ion clusters:16 (Memory usage:223MB)
2021-11-17 15:42:16,982 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_947_950_PeakCluster.serFS...
2021-11-17 15:42:16,983 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:17,219 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:17,465 INFO  [root] ==================================================================================
2021-11-17 15:42:17,465 INFO  [root] Processing DIA MS2 (mz range):944.0_947.0( 12/61 )
2021-11-17 15:42:17,508 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:17,508 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:18,167 INFO  [root] 115509 Peak curves found (Memory usage:212MB)
2021-11-17 15:42:18,169 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:18,169 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:18,590 INFO  [root] No of ion clusters:16 (Memory usage:221MB)
2021-11-17 15:42:18,590 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_944_947_PeakCluster.serFS...
2021-11-17 15:42:18,591 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:18,778 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:19,028 INFO  [root] ==================================================================================
2021-11-17 15:42:19,028 INFO  [root] Processing DIA MS2 (mz range):941.0_944.0( 13/61 )
2021-11-17 15:42:19,077 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:19,077 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:19,985 INFO  [root] 108292 Peak curves found (Memory usage:212MB)
2021-11-17 15:42:19,987 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:19,987 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:20,349 INFO  [root] No of ion clusters:14 (Memory usage:220MB)
2021-11-17 15:42:20,350 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_941_944_PeakCluster.serFS...
2021-11-17 15:42:20,350 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:20,561 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:20,817 INFO  [root] ==================================================================================
2021-11-17 15:42:20,817 INFO  [root] Processing DIA MS2 (mz range):938.0_941.0( 14/61 )
2021-11-17 15:42:20,876 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:20,876 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:21,819 INFO  [root] 129035 Peak curves found (Memory usage:222MB)
2021-11-17 15:42:21,821 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:21,821 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:22,262 INFO  [root] No of ion clusters:18 (Memory usage:232MB)
2021-11-17 15:42:22,262 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_938_941_PeakCluster.serFS...
2021-11-17 15:42:22,263 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:22,537 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:22,832 INFO  [root] ==================================================================================
2021-11-17 15:42:22,832 INFO  [root] Processing DIA MS2 (mz range):935.0_938.0( 15/61 )
2021-11-17 15:42:22,881 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:22,881 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:23,918 INFO  [root] 125063 Peak curves found (Memory usage:221MB)
2021-11-17 15:42:23,920 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:23,920 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:24,303 INFO  [root] No of ion clusters:16 (Memory usage:231MB)
2021-11-17 15:42:24,304 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_935_938_PeakCluster.serFS...
2021-11-17 15:42:24,304 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:24,539 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:24,767 INFO  [root] ==================================================================================
2021-11-17 15:42:24,767 INFO  [root] Processing DIA MS2 (mz range):932.0_935.0( 16/61 )
2021-11-17 15:42:24,805 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:24,806 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:25,484 INFO  [root] 106483 Peak curves found (Memory usage:214MB)
2021-11-17 15:42:25,486 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:25,486 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:25,873 INFO  [root] No of ion clusters:14 (Memory usage:222MB)
2021-11-17 15:42:25,874 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_932_935_PeakCluster.serFS...
2021-11-17 15:42:25,874 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:26,135 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:26,403 INFO  [root] ==================================================================================
2021-11-17 15:42:26,403 INFO  [root] Processing DIA MS2 (mz range):929.0_932.0( 17/61 )
2021-11-17 15:42:26,443 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:26,443 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:26,982 INFO  [root] 100809 Peak curves found (Memory usage:212MB)
2021-11-17 15:42:26,984 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:26,984 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:27,329 INFO  [root] No of ion clusters:9 (Memory usage:219MB)
2021-11-17 15:42:27,329 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_929_932_PeakCluster.serFS...
2021-11-17 15:42:27,329 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:27,507 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:27,737 INFO  [root] ==================================================================================
2021-11-17 15:42:27,737 INFO  [root] Processing DIA MS2 (mz range):926.0_929.0( 18/61 )
2021-11-17 15:42:27,779 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:27,779 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:28,339 INFO  [root] 96745 Peak curves found (Memory usage:211MB)
2021-11-17 15:42:28,341 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:28,341 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:28,683 INFO  [root] No of ion clusters:11 (Memory usage:219MB)
2021-11-17 15:42:28,683 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_926_929_PeakCluster.serFS...
2021-11-17 15:42:28,684 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:28,888 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:29,151 INFO  [root] ==================================================================================
2021-11-17 15:42:29,152 INFO  [root] Processing DIA MS2 (mz range):923.0_926.0( 19/61 )
2021-11-17 15:42:29,194 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:29,194 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:29,882 INFO  [root] 98970 Peak curves found (Memory usage:213MB)
2021-11-17 15:42:29,884 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:29,885 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:30,254 INFO  [root] No of ion clusters:9 (Memory usage:220MB)
2021-11-17 15:42:30,254 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_923_926_PeakCluster.serFS...
2021-11-17 15:42:30,255 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:30,437 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:30,675 INFO  [root] ==================================================================================
2021-11-17 15:42:30,675 INFO  [root] Processing DIA MS2 (mz range):920.0_923.0( 20/61 )
2021-11-17 15:42:30,717 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:30,717 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:31,237 INFO  [root] 106399 Peak curves found (Memory usage:216MB)
2021-11-17 15:42:31,239 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:31,239 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:31,602 INFO  [root] No of ion clusters:9 (Memory usage:224MB)
2021-11-17 15:42:31,602 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_920_923_PeakCluster.serFS...
2021-11-17 15:42:31,603 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:31,784 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:31,997 INFO  [root] ==================================================================================
2021-11-17 15:42:31,997 INFO  [root] Processing DIA MS2 (mz range):917.0_920.0( 21/61 )
2021-11-17 15:42:32,033 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:32,034 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:33,019 INFO  [root] 100991 Peak curves found (Memory usage:216MB)
2021-11-17 15:42:33,021 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:33,021 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:33,386 INFO  [root] No of ion clusters:7 (Memory usage:224MB)
2021-11-17 15:42:33,386 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_917_920_PeakCluster.serFS...
2021-11-17 15:42:33,387 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:33,616 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:33,851 INFO  [root] ==================================================================================
2021-11-17 15:42:33,851 INFO  [root] Processing DIA MS2 (mz range):914.0_917.0( 22/61 )
2021-11-17 15:42:33,884 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:33,884 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:34,407 INFO  [root] 99764 Peak curves found (Memory usage:215MB)
2021-11-17 15:42:34,410 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:34,410 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:34,766 INFO  [root] No of ion clusters:17 (Memory usage:222MB)
2021-11-17 15:42:34,766 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_914_917_PeakCluster.serFS...
2021-11-17 15:42:34,767 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:34,931 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:35,145 INFO  [root] ==================================================================================
2021-11-17 15:42:35,146 INFO  [root] Processing DIA MS2 (mz range):911.0_914.0( 23/61 )
2021-11-17 15:42:35,178 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:35,178 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:35,661 INFO  [root] 89039 Peak curves found (Memory usage:211MB)
2021-11-17 15:42:35,662 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:35,662 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:35,992 INFO  [root] No of ion clusters:18 (Memory usage:218MB)
2021-11-17 15:42:35,992 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_911_914_PeakCluster.serFS...
2021-11-17 15:42:35,993 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:36,131 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:36,381 INFO  [root] ==================================================================================
2021-11-17 15:42:36,381 INFO  [root] Processing DIA MS2 (mz range):908.0_911.0( 24/61 )
2021-11-17 15:42:36,418 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:36,418 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:37,032 INFO  [root] 94073 Peak curves found (Memory usage:214MB)
2021-11-17 15:42:37,034 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:37,034 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:37,368 INFO  [root] No of ion clusters:20 (Memory usage:221MB)
2021-11-17 15:42:37,368 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_908_911_PeakCluster.serFS...
2021-11-17 15:42:37,369 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:37,543 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:37,766 INFO  [root] ==================================================================================
2021-11-17 15:42:37,766 INFO  [root] Processing DIA MS2 (mz range):905.0_908.0( 25/61 )
2021-11-17 15:42:37,803 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:37,803 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:38,332 INFO  [root] 98722 Peak curves found (Memory usage:216MB)
2021-11-17 15:42:38,333 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:38,333 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:38,659 INFO  [root] No of ion clusters:17 (Memory usage:224MB)
2021-11-17 15:42:38,659 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_905_908_PeakCluster.serFS...
2021-11-17 15:42:38,660 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:38,860 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:39,112 INFO  [root] ==================================================================================
2021-11-17 15:42:39,112 INFO  [root] Processing DIA MS2 (mz range):902.0_905.0( 26/61 )
2021-11-17 15:42:39,151 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:39,152 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:39,738 INFO  [root] 113736 Peak curves found (Memory usage:223MB)
2021-11-17 15:42:39,740 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:39,740 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:40,109 INFO  [root] No of ion clusters:11 (Memory usage:232MB)
2021-11-17 15:42:40,109 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_902_905_PeakCluster.serFS...
2021-11-17 15:42:40,110 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:40,300 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:40,519 INFO  [root] ==================================================================================
2021-11-17 15:42:40,519 INFO  [root] Processing DIA MS2 (mz range):899.0_902.0( 27/61 )
2021-11-17 15:42:40,565 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:40,565 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:41,525 INFO  [root] 110058 Peak curves found (Memory usage:224MB)
2021-11-17 15:42:41,527 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:41,527 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:41,883 INFO  [root] No of ion clusters:8 (Memory usage:232MB)
2021-11-17 15:42:41,883 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_899_902_PeakCluster.serFS...
2021-11-17 15:42:41,884 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:42,128 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:42,375 INFO  [root] ==================================================================================
2021-11-17 15:42:42,375 INFO  [root] Processing DIA MS2 (mz range):896.0_899.0( 28/61 )
2021-11-17 15:42:42,419 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:42,419 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:43,142 INFO  [root] 128361 Peak curves found (Memory usage:231MB)
2021-11-17 15:42:43,144 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:43,144 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:43,528 INFO  [root] No of ion clusters:12 (Memory usage:241MB)
2021-11-17 15:42:43,528 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_896_899_PeakCluster.serFS...
2021-11-17 15:42:43,529 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:43,838 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:44,047 INFO  [root] ==================================================================================
2021-11-17 15:42:44,047 INFO  [root] Processing DIA MS2 (mz range):893.0_896.0( 29/61 )
2021-11-17 15:42:44,094 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:44,094 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:44,935 INFO  [root] 110795 Peak curves found (Memory usage:225MB)
2021-11-17 15:42:44,937 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:44,937 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:45,329 INFO  [root] No of ion clusters:8 (Memory usage:234MB)
2021-11-17 15:42:45,329 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_893_896_PeakCluster.serFS...
2021-11-17 15:42:45,330 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:45,697 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:45,948 INFO  [root] ==================================================================================
2021-11-17 15:42:45,948 INFO  [root] Processing DIA MS2 (mz range):890.0_893.0( 30/61 )
2021-11-17 15:42:45,989 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:45,989 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:46,567 INFO  [root] 117120 Peak curves found (Memory usage:226MB)
2021-11-17 15:42:46,569 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:46,569 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:46,933 INFO  [root] No of ion clusters:9 (Memory usage:235MB)
2021-11-17 15:42:46,933 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_890_893_PeakCluster.serFS...
2021-11-17 15:42:46,934 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:47,256 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:47,493 INFO  [root] ==================================================================================
2021-11-17 15:42:47,493 INFO  [root] Processing DIA MS2 (mz range):887.0_890.0( 31/61 )
2021-11-17 15:42:47,583 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:47,583 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:48,405 INFO  [root] 114204 Peak curves found (Memory usage:227MB)
2021-11-17 15:42:48,407 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:48,407 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:48,813 INFO  [root] No of ion clusters:10 (Memory usage:235MB)
2021-11-17 15:42:48,813 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_887_890_PeakCluster.serFS...
2021-11-17 15:42:48,814 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:49,113 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:49,398 INFO  [root] ==================================================================================
2021-11-17 15:42:49,398 INFO  [root] Processing DIA MS2 (mz range):884.0_887.0( 32/61 )
2021-11-17 15:42:49,445 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:49,445 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:50,262 INFO  [root] 106761 Peak curves found (Memory usage:224MB)
2021-11-17 15:42:50,263 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:50,264 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:50,613 INFO  [root] No of ion clusters:23 (Memory usage:232MB)
2021-11-17 15:42:50,613 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_884_887_PeakCluster.serFS...
2021-11-17 15:42:50,614 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:50,853 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:51,140 INFO  [root] ==================================================================================
2021-11-17 15:42:51,140 INFO  [root] Processing DIA MS2 (mz range):881.0_884.0( 33/61 )
2021-11-17 15:42:51,194 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:51,194 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:51,730 INFO  [root] 104002 Peak curves found (Memory usage:223MB)
2021-11-17 15:42:51,733 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:51,733 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:52,133 INFO  [root] No of ion clusters:7 (Memory usage:231MB)
2021-11-17 15:42:52,133 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_881_884_PeakCluster.serFS...
2021-11-17 15:42:52,134 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:52,290 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:52,511 INFO  [root] ==================================================================================
2021-11-17 15:42:52,511 INFO  [root] Processing DIA MS2 (mz range):878.0_881.0( 34/61 )
2021-11-17 15:42:52,546 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:52,547 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:53,128 INFO  [root] 102703 Peak curves found (Memory usage:223MB)
2021-11-17 15:42:53,130 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:53,130 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:53,478 INFO  [root] No of ion clusters:9 (Memory usage:231MB)
2021-11-17 15:42:53,478 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_878_881_PeakCluster.serFS...
2021-11-17 15:42:53,478 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:53,745 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:54,012 INFO  [root] ==================================================================================
2021-11-17 15:42:54,012 INFO  [root] Processing DIA MS2 (mz range):875.0_878.0( 35/61 )
2021-11-17 15:42:54,051 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:54,051 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:54,728 INFO  [root] 122827 Peak curves found (Memory usage:232MB)
2021-11-17 15:42:54,730 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:54,730 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:55,142 INFO  [root] No of ion clusters:7 (Memory usage:241MB)
2021-11-17 15:42:55,142 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_875_878_PeakCluster.serFS...
2021-11-17 15:42:55,143 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:55,478 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:55,709 INFO  [root] ==================================================================================
2021-11-17 15:42:55,709 INFO  [root] Processing DIA MS2 (mz range):872.0_875.0( 36/61 )
2021-11-17 15:42:55,754 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:55,754 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:56,996 INFO  [root] 114701 Peak curves found (Memory usage:232MB)
2021-11-17 15:42:56,998 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:56,998 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:57,354 INFO  [root] No of ion clusters:8 (Memory usage:240MB)
2021-11-17 15:42:57,354 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_872_875_PeakCluster.serFS...
2021-11-17 15:42:57,355 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:57,639 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:57,959 INFO  [root] ==================================================================================
2021-11-17 15:42:57,959 INFO  [root] Processing DIA MS2 (mz range):869.0_872.0( 37/61 )
2021-11-17 15:42:57,999 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:57,999 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:58,556 INFO  [root] 120397 Peak curves found (Memory usage:231MB)
2021-11-17 15:42:58,558 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:58,558 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:42:58,964 INFO  [root] No of ion clusters:8 (Memory usage:240MB)
2021-11-17 15:42:58,964 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_869_872_PeakCluster.serFS...
2021-11-17 15:42:58,964 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:42:59,152 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:42:59,386 INFO  [root] ==================================================================================
2021-11-17 15:42:59,386 INFO  [root] Processing DIA MS2 (mz range):866.0_869.0( 38/61 )
2021-11-17 15:42:59,420 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:42:59,420 INFO  [root] Smoothing detected signals......
2021-11-17 15:42:59,913 INFO  [root] 100707 Peak curves found (Memory usage:224MB)
2021-11-17 15:42:59,915 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:42:59,915 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:00,284 INFO  [root] No of ion clusters:10 (Memory usage:231MB)
2021-11-17 15:43:00,284 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_866_869_PeakCluster.serFS...
2021-11-17 15:43:00,285 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:00,517 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:00,772 INFO  [root] ==================================================================================
2021-11-17 15:43:00,772 INFO  [root] Processing DIA MS2 (mz range):863.0_866.0( 39/61 )
2021-11-17 15:43:00,820 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:00,820 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:01,558 INFO  [root] 110528 Peak curves found (Memory usage:229MB)
2021-11-17 15:43:01,560 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:01,560 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:01,914 INFO  [root] No of ion clusters:13 (Memory usage:237MB)
2021-11-17 15:43:01,915 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_863_866_PeakCluster.serFS...
2021-11-17 15:43:01,915 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:02,138 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:02,357 INFO  [root] ==================================================================================
2021-11-17 15:43:02,357 INFO  [root] Processing DIA MS2 (mz range):860.0_863.0( 40/61 )
2021-11-17 15:43:02,399 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:02,399 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:03,065 INFO  [root] 114782 Peak curves found (Memory usage:230MB)
2021-11-17 15:43:03,067 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:03,067 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:03,459 INFO  [root] No of ion clusters:12 (Memory usage:239MB)
2021-11-17 15:43:03,459 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_860_863_PeakCluster.serFS...
2021-11-17 15:43:03,460 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:03,708 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:03,954 INFO  [root] ==================================================================================
2021-11-17 15:43:03,954 INFO  [root] Processing DIA MS2 (mz range):857.0_860.0( 41/61 )
2021-11-17 15:43:03,999 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:03,999 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:04,790 INFO  [root] 119388 Peak curves found (Memory usage:233MB)
2021-11-17 15:43:04,792 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:04,792 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:05,213 INFO  [root] No of ion clusters:6 (Memory usage:241MB)
2021-11-17 15:43:05,213 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_857_860_PeakCluster.serFS...
2021-11-17 15:43:05,215 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:05,483 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:05,722 INFO  [root] ==================================================================================
2021-11-17 15:43:05,722 INFO  [root] Processing DIA MS2 (mz range):854.0_857.0( 42/61 )
2021-11-17 15:43:05,769 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:05,769 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:06,615 INFO  [root] 117561 Peak curves found (Memory usage:233MB)
2021-11-17 15:43:06,617 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:06,617 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:06,987 INFO  [root] No of ion clusters:5 (Memory usage:242MB)
2021-11-17 15:43:06,987 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_854_857_PeakCluster.serFS...
2021-11-17 15:43:06,988 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:07,294 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:07,549 INFO  [root] ==================================================================================
2021-11-17 15:43:07,549 INFO  [root] Processing DIA MS2 (mz range):851.0_854.0( 43/61 )
2021-11-17 15:43:07,589 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:07,589 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:08,227 INFO  [root] 125852 Peak curves found (Memory usage:235MB)
2021-11-17 15:43:08,229 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:08,229 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:08,653 INFO  [root] No of ion clusters:11 (Memory usage:245MB)
2021-11-17 15:43:08,653 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_851_854_PeakCluster.serFS...
2021-11-17 15:43:08,654 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:08,878 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:09,107 INFO  [root] ==================================================================================
2021-11-17 15:43:09,107 INFO  [root] Processing DIA MS2 (mz range):848.0_851.0( 44/61 )
2021-11-17 15:43:09,148 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:09,148 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:09,971 INFO  [root] 119014 Peak curves found (Memory usage:233MB)
2021-11-17 15:43:09,973 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:09,973 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:10,340 INFO  [root] No of ion clusters:9 (Memory usage:242MB)
2021-11-17 15:43:10,340 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_848_851_PeakCluster.serFS...
2021-11-17 15:43:10,341 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:10,627 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:10,885 INFO  [root] ==================================================================================
2021-11-17 15:43:10,885 INFO  [root] Processing DIA MS2 (mz range):845.0_848.0( 45/61 )
2021-11-17 15:43:10,933 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:10,933 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:11,715 INFO  [root] 128497 Peak curves found (Memory usage:237MB)
2021-11-17 15:43:11,718 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:11,718 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:12,151 INFO  [root] No of ion clusters:9 (Memory usage:247MB)
2021-11-17 15:43:12,151 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_845_848_PeakCluster.serFS...
2021-11-17 15:43:12,152 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:12,464 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:12,747 INFO  [root] ==================================================================================
2021-11-17 15:43:12,747 INFO  [root] Processing DIA MS2 (mz range):842.0_845.0( 46/61 )
2021-11-17 15:43:12,813 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:12,813 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:13,575 INFO  [root] 127495 Peak curves found (Memory usage:237MB)
2021-11-17 15:43:13,577 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:13,578 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:13,997 INFO  [root] No of ion clusters:12 (Memory usage:246MB)
2021-11-17 15:43:13,997 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_842_845_PeakCluster.serFS...
2021-11-17 15:43:13,998 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:14,252 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:14,499 INFO  [root] ==================================================================================
2021-11-17 15:43:14,499 INFO  [root] Processing DIA MS2 (mz range):839.0_842.0( 47/61 )
2021-11-17 15:43:14,546 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:14,546 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:15,300 INFO  [root] 139542 Peak curves found (Memory usage:242MB)
2021-11-17 15:43:15,301 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:15,301 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:15,750 INFO  [root] No of ion clusters:12 (Memory usage:253MB)
2021-11-17 15:43:15,750 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_839_842_PeakCluster.serFS...
2021-11-17 15:43:15,751 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:16,094 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:16,353 INFO  [root] ==================================================================================
2021-11-17 15:43:16,353 INFO  [root] Processing DIA MS2 (mz range):836.0_839.0( 48/61 )
2021-11-17 15:43:16,404 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:16,405 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:17,373 INFO  [root] 147110 Peak curves found (Memory usage:247MB)
2021-11-17 15:43:17,375 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:17,375 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:17,861 INFO  [root] No of ion clusters:4 (Memory usage:258MB)
2021-11-17 15:43:17,861 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_836_839_PeakCluster.serFS...
2021-11-17 15:43:17,862 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:18,301 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:18,548 INFO  [root] ==================================================================================
2021-11-17 15:43:18,548 INFO  [root] Processing DIA MS2 (mz range):833.0_836.0( 49/61 )
2021-11-17 15:43:18,595 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:18,595 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:19,551 INFO  [root] 139325 Peak curves found (Memory usage:243MB)
2021-11-17 15:43:19,553 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:19,553 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:20,016 INFO  [root] No of ion clusters:5 (Memory usage:254MB)
2021-11-17 15:43:20,016 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_833_836_PeakCluster.serFS...
2021-11-17 15:43:20,017 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:20,377 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:20,661 INFO  [root] ==================================================================================
2021-11-17 15:43:20,661 INFO  [root] Processing DIA MS2 (mz range):830.0_833.0( 50/61 )
2021-11-17 15:43:20,715 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:20,715 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:21,676 INFO  [root] 142866 Peak curves found (Memory usage:245MB)
2021-11-17 15:43:21,678 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:21,678 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:22,153 INFO  [root] No of ion clusters:14 (Memory usage:256MB)
2021-11-17 15:43:22,153 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_830_833_PeakCluster.serFS...
2021-11-17 15:43:22,154 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:22,475 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:22,770 INFO  [root] ==================================================================================
2021-11-17 15:43:22,770 INFO  [root] Processing DIA MS2 (mz range):827.0_830.0( 51/61 )
2021-11-17 15:43:22,821 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:22,821 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:24,085 INFO  [root] 133348 Peak curves found (Memory usage:242MB)
2021-11-17 15:43:24,087 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:24,087 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:24,517 INFO  [root] No of ion clusters:8 (Memory usage:253MB)
2021-11-17 15:43:24,517 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_827_830_PeakCluster.serFS...
2021-11-17 15:43:24,518 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:24,836 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:25,090 INFO  [root] ==================================================================================
2021-11-17 15:43:25,091 INFO  [root] Processing DIA MS2 (mz range):824.0_827.0( 52/61 )
2021-11-17 15:43:25,136 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:25,136 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:26,201 INFO  [root] 126283 Peak curves found (Memory usage:237MB)
2021-11-17 15:43:26,203 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:26,203 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:26,616 INFO  [root] No of ion clusters:8 (Memory usage:247MB)
2021-11-17 15:43:26,617 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_824_827_PeakCluster.serFS...
2021-11-17 15:43:26,617 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:26,874 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:27,109 INFO  [root] ==================================================================================
2021-11-17 15:43:27,109 INFO  [root] Processing DIA MS2 (mz range):821.0_824.0( 53/61 )
2021-11-17 15:43:27,155 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:27,155 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:27,938 INFO  [root] 130306 Peak curves found (Memory usage:239MB)
2021-11-17 15:43:27,939 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:27,939 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:28,341 INFO  [root] No of ion clusters:15 (Memory usage:249MB)
2021-11-17 15:43:28,341 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_821_824_PeakCluster.serFS...
2021-11-17 15:43:28,342 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:28,682 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:28,986 INFO  [root] ==================================================================================
2021-11-17 15:43:28,986 INFO  [root] Processing DIA MS2 (mz range):818.0_821.0( 54/61 )
2021-11-17 15:43:29,051 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:29,051 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:29,848 INFO  [root] 121567 Peak curves found (Memory usage:236MB)
2021-11-17 15:43:29,850 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:29,850 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:30,247 INFO  [root] No of ion clusters:10 (Memory usage:246MB)
2021-11-17 15:43:30,247 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_818_821_PeakCluster.serFS...
2021-11-17 15:43:30,248 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:30,549 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:30,793 INFO  [root] ==================================================================================
2021-11-17 15:43:30,793 INFO  [root] Processing DIA MS2 (mz range):815.0_818.0( 55/61 )
2021-11-17 15:43:30,832 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:30,832 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:31,589 INFO  [root] 117397 Peak curves found (Memory usage:234MB)
2021-11-17 15:43:31,591 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:31,591 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:31,974 INFO  [root] No of ion clusters:9 (Memory usage:243MB)
2021-11-17 15:43:31,974 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_815_818_PeakCluster.serFS...
2021-11-17 15:43:31,975 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:32,231 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:32,483 INFO  [root] ==================================================================================
2021-11-17 15:43:32,483 INFO  [root] Processing DIA MS2 (mz range):812.0_815.0( 56/61 )
2021-11-17 15:43:32,530 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:32,530 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:33,162 INFO  [root] 115442 Peak curves found (Memory usage:233MB)
2021-11-17 15:43:33,164 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:33,164 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:33,537 INFO  [root] No of ion clusters:15 (Memory usage:242MB)
2021-11-17 15:43:33,538 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_812_815_PeakCluster.serFS...
2021-11-17 15:43:33,538 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:33,780 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:34,038 INFO  [root] ==================================================================================
2021-11-17 15:43:34,038 INFO  [root] Processing DIA MS2 (mz range):809.0_812.0( 57/61 )
2021-11-17 15:43:34,076 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:34,076 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:34,687 INFO  [root] 111805 Peak curves found (Memory usage:232MB)
2021-11-17 15:43:34,689 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:34,689 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:35,137 INFO  [root] No of ion clusters:7 (Memory usage:240MB)
2021-11-17 15:43:35,137 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_809_812_PeakCluster.serFS...
2021-11-17 15:43:35,138 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:35,435 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:35,671 INFO  [root] ==================================================================================
2021-11-17 15:43:35,671 INFO  [root] Processing DIA MS2 (mz range):806.0_809.0( 58/61 )
2021-11-17 15:43:35,714 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:35,714 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:36,366 INFO  [root] 121859 Peak curves found (Memory usage:236MB)
2021-11-17 15:43:36,368 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:36,368 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:36,753 INFO  [root] No of ion clusters:13 (Memory usage:245MB)
2021-11-17 15:43:36,753 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_806_809_PeakCluster.serFS...
2021-11-17 15:43:36,754 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:37,065 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:37,351 INFO  [root] ==================================================================================
2021-11-17 15:43:37,351 INFO  [root] Processing DIA MS2 (mz range):803.0_806.0( 59/61 )
2021-11-17 15:43:37,406 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:37,406 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:38,170 INFO  [root] 125374 Peak curves found (Memory usage:238MB)
2021-11-17 15:43:38,171 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:38,172 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:38,657 INFO  [root] No of ion clusters:6 (Memory usage:247MB)
2021-11-17 15:43:38,657 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_803_806_PeakCluster.serFS...
2021-11-17 15:43:38,658 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:38,993 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:39,235 INFO  [root] ==================================================================================
2021-11-17 15:43:39,235 INFO  [root] Processing DIA MS2 (mz range):800.0_803.0( 60/61 )
2021-11-17 15:43:39,270 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:39,270 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:39,854 INFO  [root] 75921 Peak curves found (Memory usage:219MB)
2021-11-17 15:43:39,857 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:39,857 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:40,194 INFO  [root] No of ion clusters:8 (Memory usage:225MB)
2021-11-17 15:43:40,194 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_800_803_PeakCluster.serFS...
2021-11-17 15:43:40,195 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:40,465 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:40,705 INFO  [root] ==================================================================================
2021-11-17 15:43:40,705 INFO  [root] Processing DIA MS2 (mz range):797.0_800.0( 61/61 )
2021-11-17 15:43:40,728 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:40,728 INFO  [root] Smoothing detected signals......
2021-11-17 15:43:41,756 INFO  [root] 60862 Peak curves found (Memory usage:217MB)
2021-11-17 15:43:41,758 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:43:41,758 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:43:42,034 INFO  [root] No of ion clusters:45 (Memory usage:222MB)
2021-11-17 15:43:42,035 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_797_800_PeakCluster.serFS...
2021-11-17 15:43:42,035 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:43:42,564 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:43:43,044 INFO  [root] ==================================================================================
2021-11-17 15:43:44,330 INFO  [root] C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.mzXML processed time:0 hour, 2 min, 8 sec
2021-11-17 15:43:44,330 INFO  [root] Job complete
2021-11-17 15:43:44,330 INFO  [root] =================================================================================================
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
=================================================================================================
DIA-Umpire singal extraction analysis  (version: v2.2.3)
(c) University of Michigan
2021-11-17 15:43:51,494 INFO  [root] Version: v2.2.3
2021-11-17 15:43:51,495 INFO  [root] Parameter file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
2021-11-17 15:43:51,495 INFO  [root] Spectra file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.mzXML
2021-11-17 15:43:51,497 INFO  [root] 
2021-11-17 15:43:51,497 INFO  [root] ####################################################################################################
2021-11-17 15:43:51,497 INFO  [root] #No of threads
2021-11-17 15:43:51,497 INFO  [root] Thread = 7
2021-11-17 15:43:51,498 INFO  [root] ####################################################################################################
2021-11-17 15:43:51,498 INFO  [root] 
2021-11-17 15:43:51,498 INFO  [root] ## omit Thread
2021-11-17 15:43:51,498 INFO  [root] 
2021-11-17 15:43:51,498 INFO  [root] #Precursor-fragments grouping parameters
2021-11-17 15:43:51,498 INFO  [root] RPmax = 25
2021-11-17 15:43:51,498 INFO  [root] RFmax = 500
2021-11-17 15:43:51,498 INFO  [root] CorrThreshold = 0
2021-11-17 15:43:51,498 INFO  [root] DeltaApex = 0.2
2021-11-17 15:43:51,499 INFO  [root] RTOverlap = 0.3
2021-11-17 15:43:51,499 INFO  [root] 
2021-11-17 15:43:51,499 INFO  [root] #Fragment intensity adjustments
2021-11-17 15:43:51,499 INFO  [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2021-11-17 15:43:51,499 INFO  [root] AdjustFragIntensity = true
2021-11-17 15:43:51,499 INFO  [root] BoostComplementaryIon = false
2021-11-17 15:43:51,499 INFO  [root] 
2021-11-17 15:43:51,499 INFO  [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2021-11-17 15:43:51,499 INFO  [root] ExportPrecursorPeak = false
2021-11-17 15:43:51,499 INFO  [root] 
2021-11-17 15:43:51,499 INFO  [root] Q1 = true
2021-11-17 15:43:51,499 INFO  [root] Q2 = true
2021-11-17 15:43:51,499 INFO  [root] Q3 = true
2021-11-17 15:43:51,499 INFO  [root] 
2021-11-17 15:43:51,499 INFO  [root] #Signal extraction: mass accuracy and resolution
2021-11-17 15:43:51,499 INFO  [root] # resolution parameter matters only for data generated in profile mode
2021-11-17 15:43:51,500 INFO  [root] SE.MS1PPM = 10
2021-11-17 15:43:51,500 INFO  [root] SE.MS2PPM = 10
2021-11-17 15:43:51,500 INFO  [root] SE.Resolution = 60000
2021-11-17 15:43:51,500 INFO  [root] 
2021-11-17 15:43:51,500 INFO  [root] #Signal extraction: signal to noise filter
2021-11-17 15:43:51,500 INFO  [root] SE.SN = 1.1
2021-11-17 15:43:51,500 INFO  [root] SE.MS2SN = 1.1
2021-11-17 15:43:51,500 INFO  [root] 
2021-11-17 15:43:51,500 INFO  [root] #Signal extraction: minimum signal intensity filter
2021-11-17 15:43:51,500 INFO  [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2021-11-17 15:43:51,500 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2021-11-17 15:43:51,500 INFO  [root] SE.EstimateBG = false
2021-11-17 15:43:51,501 INFO  [root] SE.MinMSIntensity = 1
2021-11-17 15:43:51,501 INFO  [root] SE.MinMSMSIntensity = 1
2021-11-17 15:43:51,501 INFO  [root] 
2021-11-17 15:43:51,501 INFO  [root] #Signal extraction: peak curve detection and isotope grouping
2021-11-17 15:43:51,501 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2021-11-17 15:43:51,501 INFO  [root] SE.NoMissedScan = 1
2021-11-17 15:43:51,501 INFO  [root] SE.MaxCurveRTRange = 2
2021-11-17 15:43:51,501 INFO  [root] SE.RemoveGroupedPeaks = true
2021-11-17 15:43:51,501 INFO  [root] SE.RemoveGroupedPeaksRTOverlap = 0.3
2021-11-17 15:43:51,519 INFO  [root] SE.RemoveGroupedPeaksCorr = 0.3
2021-11-17 15:43:51,519 INFO  [root] SE.MinNoPeakCluster = 2
2021-11-17 15:43:51,519 INFO  [root] SE.MaxNoPeakCluster = 4
2021-11-17 15:43:51,519 INFO  [root] 
2021-11-17 15:43:51,519 INFO  [root] #Signal extraction: filtering of MS1 features
2021-11-17 15:43:51,519 INFO  [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2021-11-17 15:43:51,519 INFO  [root] SE.IsoPattern = 0.3
2021-11-17 15:43:51,519 INFO  [root] SE.MassDefectFilter = false
2021-11-17 15:43:51,520 INFO  [root] SE.MassDefectOffset = 0.1
2021-11-17 15:43:51,520 INFO  [root] 
2021-11-17 15:43:51,520 INFO  [root] #Signal extraction: other
2021-11-17 15:43:51,520 INFO  [root] SE.StartCharge = 1
2021-11-17 15:43:51,520 INFO  [root] SE.EndCharge = 5
2021-11-17 15:43:51,520 INFO  [root] SE.MS2StartCharge = 2
2021-11-17 15:43:51,520 INFO  [root] SE.MS2EndCharge = 5
2021-11-17 15:43:51,520 INFO  [root] SE.MinFrag = 10
2021-11-17 15:43:51,520 INFO  [root] SE.StartRT = 0
2021-11-17 15:43:51,520 INFO  [root] SE.EndRT = 9999
2021-11-17 15:43:51,520 INFO  [root] SE.MinMZ = 200
2021-11-17 15:43:51,520 INFO  [root] SE.MinPrecursorMass = 600
2021-11-17 15:43:51,521 INFO  [root] SE.MaxPrecursorMass = 5000
2021-11-17 15:43:51,521 INFO  [root] 
2021-11-17 15:43:51,521 INFO  [root] 
2021-11-17 15:43:51,521 INFO  [root] #Isolation window setting
2021-11-17 15:43:51,521 INFO  [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2021-11-17 15:43:51,521 INFO  [root] WindowType = SWATH
2021-11-17 15:43:51,521 INFO  [root] 
2021-11-17 15:43:51,521 INFO  [root] #Fix window size (For SWATH)
2021-11-17 15:43:51,521 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:43:51,521 INFO  [root] WindowSize = 10
2021-11-17 15:43:51,521 INFO  [root] 
2021-11-17 15:43:51,521 INFO  [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2021-11-17 15:43:51,521 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:43:51,521 INFO  [root] ==window setting begin
2021-11-17 15:43:51,521 INFO  [root] 
2021-11-17 15:43:51,521 INFO  [root] =================================================================================================
2021-11-17 15:43:51,522 INFO  [root] Processing C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.mzXML....
2021-11-17 15:43:51,526 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_diasetting.ser...
2021-11-17 15:43:51,534 INFO  [root] Writing parameter to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_params.ser...
2021-11-17 15:43:51,536 INFO  [root] Module A: Signal extraction
2021-11-17 15:43:54,643 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_diasetting.ser...
2021-11-17 15:43:55,095 INFO  [root] Processing MS1 peak detection
2021-11-17 15:43:55,095 INFO  [root] MS1 average cycle time : 2.6817362 seconds
2021-11-17 15:43:58,518 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:43:58,518 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:02,395 INFO  [root] 290377 Peak curves found (Memory usage:240MB)
2021-11-17 15:44:02,395 INFO  [root] Inclusion mz values found: 0/0
2021-11-17 15:44:02,395 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:02,396 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:10,661 INFO  [root] No of ion clusters:22514 (Memory usage:175MB)
2021-11-17 15:44:10,676 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_PeakCluster.serFS...
2021-11-17 15:44:10,913 INFO  [root] ==================================================================================
2021-11-17 15:44:10,913 INFO  [root] Processing DIA MS2 (mz range):977.0_980.0( 1/61 )
2021-11-17 15:44:10,998 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:10,998 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:11,772 INFO  [root] 43418 Peak curves found (Memory usage:208MB)
2021-11-17 15:44:11,775 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:11,775 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:12,058 INFO  [root] No of ion clusters:14 (Memory usage:211MB)
2021-11-17 15:44:12,058 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_977_980_PeakCluster.serFS...
2021-11-17 15:44:12,059 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:12,649 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:13,144 INFO  [root] ==================================================================================
2021-11-17 15:44:13,145 INFO  [root] Processing DIA MS2 (mz range):974.0_977.0( 2/61 )
2021-11-17 15:44:13,229 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:13,229 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:13,978 INFO  [root] 49551 Peak curves found (Memory usage:198MB)
2021-11-17 15:44:13,982 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:13,982 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:14,257 INFO  [root] No of ion clusters:11 (Memory usage:202MB)
2021-11-17 15:44:14,257 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_974_977_PeakCluster.serFS...
2021-11-17 15:44:14,258 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:14,428 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:14,694 INFO  [root] ==================================================================================
2021-11-17 15:44:14,694 INFO  [root] Processing DIA MS2 (mz range):971.0_974.0( 3/61 )
2021-11-17 15:44:14,745 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:14,745 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:15,401 INFO  [root] 82263 Peak curves found (Memory usage:211MB)
2021-11-17 15:44:15,403 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:15,404 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:15,766 INFO  [root] No of ion clusters:7 (Memory usage:218MB)
2021-11-17 15:44:15,766 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_971_974_PeakCluster.serFS...
2021-11-17 15:44:15,767 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:15,977 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:16,232 INFO  [root] ==================================================================================
2021-11-17 15:44:16,232 INFO  [root] Processing DIA MS2 (mz range):968.0_971.0( 4/61 )
2021-11-17 15:44:16,271 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:16,271 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:16,775 INFO  [root] 87191 Peak curves found (Memory usage:213MB)
2021-11-17 15:44:16,777 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:16,777 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:17,126 INFO  [root] No of ion clusters:14 (Memory usage:219MB)
2021-11-17 15:44:17,126 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_968_971_PeakCluster.serFS...
2021-11-17 15:44:17,128 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:17,252 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:17,489 INFO  [root] ==================================================================================
2021-11-17 15:44:17,489 INFO  [root] Processing DIA MS2 (mz range):965.0_968.0( 5/61 )
2021-11-17 15:44:17,532 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:17,532 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:18,145 INFO  [root] 97635 Peak curves found (Memory usage:217MB)
2021-11-17 15:44:18,147 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:18,147 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:18,525 INFO  [root] No of ion clusters:8 (Memory usage:225MB)
2021-11-17 15:44:18,525 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_965_968_PeakCluster.serFS...
2021-11-17 15:44:18,526 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:18,861 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:19,096 INFO  [root] ==================================================================================
2021-11-17 15:44:19,096 INFO  [root] Processing DIA MS2 (mz range):962.0_965.0( 6/61 )
2021-11-17 15:44:19,137 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:19,137 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:19,836 INFO  [root] 118950 Peak curves found (Memory usage:228MB)
2021-11-17 15:44:19,838 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:19,838 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:20,231 INFO  [root] No of ion clusters:16 (Memory usage:237MB)
2021-11-17 15:44:20,232 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_962_965_PeakCluster.serFS...
2021-11-17 15:44:20,232 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:20,652 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:20,945 INFO  [root] ==================================================================================
2021-11-17 15:44:20,945 INFO  [root] Processing DIA MS2 (mz range):959.0_962.0( 7/61 )
2021-11-17 15:44:20,987 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:20,987 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:21,691 INFO  [root] 116523 Peak curves found (Memory usage:228MB)
2021-11-17 15:44:21,696 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:21,696 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:22,140 INFO  [root] No of ion clusters:10 (Memory usage:237MB)
2021-11-17 15:44:22,140 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_959_962_PeakCluster.serFS...
2021-11-17 15:44:22,141 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:22,465 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:22,731 INFO  [root] ==================================================================================
2021-11-17 15:44:22,731 INFO  [root] Processing DIA MS2 (mz range):956.0_959.0( 8/61 )
2021-11-17 15:44:22,774 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:22,774 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:23,324 INFO  [root] 127133 Peak curves found (Memory usage:232MB)
2021-11-17 15:44:23,327 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:23,327 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:23,765 INFO  [root] No of ion clusters:8 (Memory usage:242MB)
2021-11-17 15:44:23,765 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_956_959_PeakCluster.serFS...
2021-11-17 15:44:23,766 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:24,065 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:24,296 INFO  [root] ==================================================================================
2021-11-17 15:44:24,296 INFO  [root] Processing DIA MS2 (mz range):953.0_956.0( 9/61 )
2021-11-17 15:44:24,340 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:24,340 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:26,053 INFO  [root] 119767 Peak curves found (Memory usage:232MB)
2021-11-17 15:44:26,055 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:26,055 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:26,550 INFO  [root] No of ion clusters:25 (Memory usage:241MB)
2021-11-17 15:44:26,550 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_953_956_PeakCluster.serFS...
2021-11-17 15:44:26,551 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:26,873 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:27,122 INFO  [root] ==================================================================================
2021-11-17 15:44:27,123 INFO  [root] Processing DIA MS2 (mz range):950.0_953.0( 10/61 )
2021-11-17 15:44:27,174 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:27,175 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:28,036 INFO  [root] 122545 Peak curves found (Memory usage:233MB)
2021-11-17 15:44:28,037 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:28,037 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:28,460 INFO  [root] No of ion clusters:11 (Memory usage:242MB)
2021-11-17 15:44:28,460 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_950_953_PeakCluster.serFS...
2021-11-17 15:44:28,461 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:28,730 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:29,007 INFO  [root] ==================================================================================
2021-11-17 15:44:29,007 INFO  [root] Processing DIA MS2 (mz range):947.0_950.0( 11/61 )
2021-11-17 15:44:29,045 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:29,045 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:29,733 INFO  [root] 98250 Peak curves found (Memory usage:224MB)
2021-11-17 15:44:29,735 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:29,735 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:30,076 INFO  [root] No of ion clusters:25 (Memory usage:232MB)
2021-11-17 15:44:30,076 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_947_950_PeakCluster.serFS...
2021-11-17 15:44:30,077 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:30,252 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:30,571 INFO  [root] ==================================================================================
2021-11-17 15:44:30,571 INFO  [root] Processing DIA MS2 (mz range):944.0_947.0( 12/61 )
2021-11-17 15:44:30,604 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:30,604 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:31,071 INFO  [root] 93566 Peak curves found (Memory usage:222MB)
2021-11-17 15:44:31,073 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:31,073 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:31,403 INFO  [root] No of ion clusters:16 (Memory usage:229MB)
2021-11-17 15:44:31,403 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_944_947_PeakCluster.serFS...
2021-11-17 15:44:31,404 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:31,516 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:31,778 INFO  [root] ==================================================================================
2021-11-17 15:44:31,779 INFO  [root] Processing DIA MS2 (mz range):941.0_944.0( 13/61 )
2021-11-17 15:44:31,828 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:31,829 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:32,690 INFO  [root] 92641 Peak curves found (Memory usage:223MB)
2021-11-17 15:44:32,691 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:32,691 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:33,103 INFO  [root] No of ion clusters:8 (Memory usage:230MB)
2021-11-17 15:44:33,103 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_941_944_PeakCluster.serFS...
2021-11-17 15:44:33,104 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:33,245 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:33,471 INFO  [root] ==================================================================================
2021-11-17 15:44:33,471 INFO  [root] Processing DIA MS2 (mz range):938.0_941.0( 14/61 )
2021-11-17 15:44:33,510 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:33,511 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:34,324 INFO  [root] 109146 Peak curves found (Memory usage:230MB)
2021-11-17 15:44:34,326 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:34,326 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:34,701 INFO  [root] No of ion clusters:14 (Memory usage:239MB)
2021-11-17 15:44:34,701 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_938_941_PeakCluster.serFS...
2021-11-17 15:44:34,702 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:34,851 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:35,079 INFO  [root] ==================================================================================
2021-11-17 15:44:35,080 INFO  [root] Processing DIA MS2 (mz range):935.0_938.0( 15/61 )
2021-11-17 15:44:35,125 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:35,125 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:35,919 INFO  [root] 107337 Peak curves found (Memory usage:231MB)
2021-11-17 15:44:35,921 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:35,921 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:36,289 INFO  [root] No of ion clusters:15 (Memory usage:239MB)
2021-11-17 15:44:36,289 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_935_938_PeakCluster.serFS...
2021-11-17 15:44:36,290 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:36,493 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:36,761 INFO  [root] ==================================================================================
2021-11-17 15:44:36,761 INFO  [root] Processing DIA MS2 (mz range):932.0_935.0( 16/61 )
2021-11-17 15:44:36,794 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:36,794 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:37,393 INFO  [root] 94658 Peak curves found (Memory usage:226MB)
2021-11-17 15:44:37,395 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:37,395 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:37,811 INFO  [root] No of ion clusters:16 (Memory usage:233MB)
2021-11-17 15:44:37,811 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_932_935_PeakCluster.serFS...
2021-11-17 15:44:37,812 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:37,994 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:38,244 INFO  [root] ==================================================================================
2021-11-17 15:44:38,244 INFO  [root] Processing DIA MS2 (mz range):929.0_932.0( 17/61 )
2021-11-17 15:44:38,276 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:38,276 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:38,723 INFO  [root] 87991 Peak curves found (Memory usage:223MB)
2021-11-17 15:44:38,725 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:38,725 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:39,083 INFO  [root] No of ion clusters:9 (Memory usage:230MB)
2021-11-17 15:44:39,083 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_929_932_PeakCluster.serFS...
2021-11-17 15:44:39,084 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:39,243 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:39,486 INFO  [root] ==================================================================================
2021-11-17 15:44:39,486 INFO  [root] Processing DIA MS2 (mz range):926.0_929.0( 18/61 )
2021-11-17 15:44:39,519 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:39,519 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:40,013 INFO  [root] 87204 Peak curves found (Memory usage:224MB)
2021-11-17 15:44:40,015 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:40,015 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:40,397 INFO  [root] No of ion clusters:9 (Memory usage:230MB)
2021-11-17 15:44:40,398 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_926_929_PeakCluster.serFS...
2021-11-17 15:44:40,399 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:40,548 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:40,773 INFO  [root] ==================================================================================
2021-11-17 15:44:40,773 INFO  [root] Processing DIA MS2 (mz range):923.0_926.0( 19/61 )
2021-11-17 15:44:40,807 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:40,807 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:41,272 INFO  [root] 80812 Peak curves found (Memory usage:222MB)
2021-11-17 15:44:41,275 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:41,275 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:41,600 INFO  [root] No of ion clusters:15 (Memory usage:228MB)
2021-11-17 15:44:41,600 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_923_926_PeakCluster.serFS...
2021-11-17 15:44:41,601 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:41,728 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:41,955 INFO  [root] ==================================================================================
2021-11-17 15:44:41,955 INFO  [root] Processing DIA MS2 (mz range):920.0_923.0( 20/61 )
2021-11-17 15:44:41,989 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:41,989 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:42,488 INFO  [root] 87026 Peak curves found (Memory usage:225MB)
2021-11-17 15:44:42,491 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:42,491 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:42,852 INFO  [root] No of ion clusters:17 (Memory usage:232MB)
2021-11-17 15:44:42,852 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_920_923_PeakCluster.serFS...
2021-11-17 15:44:42,852 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:43,002 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:43,261 INFO  [root] ==================================================================================
2021-11-17 15:44:43,261 INFO  [root] Processing DIA MS2 (mz range):917.0_920.0( 21/61 )
2021-11-17 15:44:43,292 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:43,292 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:43,880 INFO  [root] 88002 Peak curves found (Memory usage:226MB)
2021-11-17 15:44:43,881 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:43,882 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:44,225 INFO  [root] No of ion clusters:14 (Memory usage:233MB)
2021-11-17 15:44:44,226 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_917_920_PeakCluster.serFS...
2021-11-17 15:44:44,227 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:44,445 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:44,686 INFO  [root] ==================================================================================
2021-11-17 15:44:44,686 INFO  [root] Processing DIA MS2 (mz range):914.0_917.0( 22/61 )
2021-11-17 15:44:44,718 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:44,718 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:45,215 INFO  [root] 87410 Peak curves found (Memory usage:226MB)
2021-11-17 15:44:45,216 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:45,217 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:45,543 INFO  [root] No of ion clusters:10 (Memory usage:232MB)
2021-11-17 15:44:45,543 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_914_917_PeakCluster.serFS...
2021-11-17 15:44:45,544 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:45,685 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:45,938 INFO  [root] ==================================================================================
2021-11-17 15:44:45,938 INFO  [root] Processing DIA MS2 (mz range):911.0_914.0( 23/61 )
2021-11-17 15:44:45,994 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:45,994 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:46,415 INFO  [root] 84576 Peak curves found (Memory usage:225MB)
2021-11-17 15:44:46,416 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:46,417 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:46,734 INFO  [root] No of ion clusters:14 (Memory usage:231MB)
2021-11-17 15:44:46,734 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_911_914_PeakCluster.serFS...
2021-11-17 15:44:46,735 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:46,866 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:47,106 INFO  [root] ==================================================================================
2021-11-17 15:44:47,106 INFO  [root] Processing DIA MS2 (mz range):908.0_911.0( 24/61 )
2021-11-17 15:44:47,139 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:47,139 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:47,530 INFO  [root] 80983 Peak curves found (Memory usage:224MB)
2021-11-17 15:44:47,531 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:47,531 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:47,898 INFO  [root] No of ion clusters:16 (Memory usage:230MB)
2021-11-17 15:44:47,898 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_908_911_PeakCluster.serFS...
2021-11-17 15:44:47,898 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:48,028 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:48,262 INFO  [root] ==================================================================================
2021-11-17 15:44:48,262 INFO  [root] Processing DIA MS2 (mz range):905.0_908.0( 25/61 )
2021-11-17 15:44:48,292 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:48,292 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:48,674 INFO  [root] 80540 Peak curves found (Memory usage:224MB)
2021-11-17 15:44:48,676 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:48,676 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:48,984 INFO  [root] No of ion clusters:15 (Memory usage:230MB)
2021-11-17 15:44:48,984 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_905_908_PeakCluster.serFS...
2021-11-17 15:44:48,985 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:49,090 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:49,350 INFO  [root] ==================================================================================
2021-11-17 15:44:49,350 INFO  [root] Processing DIA MS2 (mz range):902.0_905.0( 26/61 )
2021-11-17 15:44:49,388 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:49,388 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:49,944 INFO  [root] 81161 Peak curves found (Memory usage:225MB)
2021-11-17 15:44:49,946 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:49,946 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:50,260 INFO  [root] No of ion clusters:15 (Memory usage:231MB)
2021-11-17 15:44:50,260 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_902_905_PeakCluster.serFS...
2021-11-17 15:44:50,261 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:50,366 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:50,587 INFO  [root] ==================================================================================
2021-11-17 15:44:50,587 INFO  [root] Processing DIA MS2 (mz range):899.0_902.0( 27/61 )
2021-11-17 15:44:50,618 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:50,618 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:51,109 INFO  [root] 81256 Peak curves found (Memory usage:226MB)
2021-11-17 15:44:51,110 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:51,110 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:51,422 INFO  [root] No of ion clusters:7 (Memory usage:232MB)
2021-11-17 15:44:51,422 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_899_902_PeakCluster.serFS...
2021-11-17 15:44:51,423 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:51,536 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:51,779 INFO  [root] ==================================================================================
2021-11-17 15:44:51,779 INFO  [root] Processing DIA MS2 (mz range):896.0_899.0( 28/61 )
2021-11-17 15:44:51,812 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:51,812 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:52,300 INFO  [root] 93729 Peak curves found (Memory usage:231MB)
2021-11-17 15:44:52,302 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:52,302 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:52,660 INFO  [root] No of ion clusters:17 (Memory usage:238MB)
2021-11-17 15:44:52,660 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_896_899_PeakCluster.serFS...
2021-11-17 15:44:52,661 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:52,808 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:53,042 INFO  [root] ==================================================================================
2021-11-17 15:44:53,043 INFO  [root] Processing DIA MS2 (mz range):893.0_896.0( 29/61 )
2021-11-17 15:44:53,079 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:53,079 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:53,540 INFO  [root] 95903 Peak curves found (Memory usage:233MB)
2021-11-17 15:44:53,542 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:53,542 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:53,905 INFO  [root] No of ion clusters:11 (Memory usage:240MB)
2021-11-17 15:44:53,906 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_893_896_PeakCluster.serFS...
2021-11-17 15:44:53,906 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:54,108 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:54,395 INFO  [root] ==================================================================================
2021-11-17 15:44:54,395 INFO  [root] Processing DIA MS2 (mz range):890.0_893.0( 30/61 )
2021-11-17 15:44:54,434 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:54,434 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:54,884 INFO  [root] 93816 Peak curves found (Memory usage:232MB)
2021-11-17 15:44:54,886 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:54,886 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:55,298 INFO  [root] No of ion clusters:10 (Memory usage:239MB)
2021-11-17 15:44:55,298 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_890_893_PeakCluster.serFS...
2021-11-17 15:44:55,299 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:55,462 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:55,730 INFO  [root] ==================================================================================
2021-11-17 15:44:55,730 INFO  [root] Processing DIA MS2 (mz range):887.0_890.0( 31/61 )
2021-11-17 15:44:55,759 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:55,759 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:56,167 INFO  [root] 78790 Peak curves found (Memory usage:227MB)
2021-11-17 15:44:56,168 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:56,168 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:56,510 INFO  [root] No of ion clusters:13 (Memory usage:233MB)
2021-11-17 15:44:56,510 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_887_890_PeakCluster.serFS...
2021-11-17 15:44:56,510 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:56,612 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:56,838 INFO  [root] ==================================================================================
2021-11-17 15:44:56,838 INFO  [root] Processing DIA MS2 (mz range):884.0_887.0( 32/61 )
2021-11-17 15:44:56,865 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:56,865 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:57,215 INFO  [root] 70240 Peak curves found (Memory usage:224MB)
2021-11-17 15:44:57,217 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:57,217 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:57,524 INFO  [root] No of ion clusters:8 (Memory usage:229MB)
2021-11-17 15:44:57,524 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_884_887_PeakCluster.serFS...
2021-11-17 15:44:57,525 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:57,650 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:57,895 INFO  [root] ==================================================================================
2021-11-17 15:44:57,895 INFO  [root] Processing DIA MS2 (mz range):881.0_884.0( 33/61 )
2021-11-17 15:44:57,931 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:57,931 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:58,270 INFO  [root] 68013 Peak curves found (Memory usage:224MB)
2021-11-17 15:44:58,273 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:58,273 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:58,541 INFO  [root] No of ion clusters:7 (Memory usage:228MB)
2021-11-17 15:44:58,541 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_881_884_PeakCluster.serFS...
2021-11-17 15:44:58,542 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:58,647 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:44:58,948 INFO  [root] ==================================================================================
2021-11-17 15:44:58,948 INFO  [root] Processing DIA MS2 (mz range):878.0_881.0( 34/61 )
2021-11-17 15:44:58,979 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:44:58,979 INFO  [root] Smoothing detected signals......
2021-11-17 15:44:59,352 INFO  [root] 69004 Peak curves found (Memory usage:223MB)
2021-11-17 15:44:59,354 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:44:59,354 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:44:59,683 INFO  [root] No of ion clusters:8 (Memory usage:229MB)
2021-11-17 15:44:59,683 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_878_881_PeakCluster.serFS...
2021-11-17 15:44:59,684 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:44:59,788 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:00,047 INFO  [root] ==================================================================================
2021-11-17 15:45:00,047 INFO  [root] Processing DIA MS2 (mz range):875.0_878.0( 35/61 )
2021-11-17 15:45:00,086 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:00,086 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:00,553 INFO  [root] 79086 Peak curves found (Memory usage:228MB)
2021-11-17 15:45:00,555 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:00,555 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:00,885 INFO  [root] No of ion clusters:6 (Memory usage:234MB)
2021-11-17 15:45:00,885 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_875_878_PeakCluster.serFS...
2021-11-17 15:45:00,886 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:01,003 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:01,231 INFO  [root] ==================================================================================
2021-11-17 15:45:01,231 INFO  [root] Processing DIA MS2 (mz range):872.0_875.0( 36/61 )
2021-11-17 15:45:01,285 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:01,285 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:01,893 INFO  [root] 80974 Peak curves found (Memory usage:230MB)
2021-11-17 15:45:01,895 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:01,895 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:02,226 INFO  [root] No of ion clusters:8 (Memory usage:236MB)
2021-11-17 15:45:02,227 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_872_875_PeakCluster.serFS...
2021-11-17 15:45:02,227 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:02,371 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:02,599 INFO  [root] ==================================================================================
2021-11-17 15:45:02,600 INFO  [root] Processing DIA MS2 (mz range):869.0_872.0( 37/61 )
2021-11-17 15:45:02,631 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:02,631 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:03,095 INFO  [root] 81821 Peak curves found (Memory usage:230MB)
2021-11-17 15:45:03,096 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:03,097 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:03,428 INFO  [root] No of ion clusters:9 (Memory usage:236MB)
2021-11-17 15:45:03,428 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_869_872_PeakCluster.serFS...
2021-11-17 15:45:03,429 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:03,542 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:03,784 INFO  [root] ==================================================================================
2021-11-17 15:45:03,785 INFO  [root] Processing DIA MS2 (mz range):866.0_869.0( 38/61 )
2021-11-17 15:45:03,813 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:03,813 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:04,184 INFO  [root] 75869 Peak curves found (Memory usage:228MB)
2021-11-17 15:45:04,186 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:04,186 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:04,507 INFO  [root] No of ion clusters:12 (Memory usage:234MB)
2021-11-17 15:45:04,507 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_866_869_PeakCluster.serFS...
2021-11-17 15:45:04,508 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:04,638 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:04,874 INFO  [root] ==================================================================================
2021-11-17 15:45:04,874 INFO  [root] Processing DIA MS2 (mz range):863.0_866.0( 39/61 )
2021-11-17 15:45:04,907 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:04,907 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:05,318 INFO  [root] 82758 Peak curves found (Memory usage:231MB)
2021-11-17 15:45:05,320 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:05,320 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:05,664 INFO  [root] No of ion clusters:13 (Memory usage:237MB)
2021-11-17 15:45:05,664 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_863_866_PeakCluster.serFS...
2021-11-17 15:45:05,665 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:05,826 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:06,120 INFO  [root] ==================================================================================
2021-11-17 15:45:06,121 INFO  [root] Processing DIA MS2 (mz range):860.0_863.0( 40/61 )
2021-11-17 15:45:06,153 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:06,153 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:06,601 INFO  [root] 86388 Peak curves found (Memory usage:233MB)
2021-11-17 15:45:06,603 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:06,603 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:06,954 INFO  [root] No of ion clusters:13 (Memory usage:240MB)
2021-11-17 15:45:06,954 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_860_863_PeakCluster.serFS...
2021-11-17 15:45:06,955 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:07,172 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:07,446 INFO  [root] ==================================================================================
2021-11-17 15:45:07,446 INFO  [root] Processing DIA MS2 (mz range):857.0_860.0( 41/61 )
2021-11-17 15:45:07,477 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:07,477 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:07,927 INFO  [root] 89747 Peak curves found (Memory usage:235MB)
2021-11-17 15:45:07,929 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:07,929 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:08,275 INFO  [root] No of ion clusters:12 (Memory usage:241MB)
2021-11-17 15:45:08,275 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_857_860_PeakCluster.serFS...
2021-11-17 15:45:08,275 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:08,406 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:08,650 INFO  [root] ==================================================================================
2021-11-17 15:45:08,650 INFO  [root] Processing DIA MS2 (mz range):854.0_857.0( 42/61 )
2021-11-17 15:45:08,682 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:08,682 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:09,176 INFO  [root] 82508 Peak curves found (Memory usage:233MB)
2021-11-17 15:45:09,178 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:09,178 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:09,502 INFO  [root] No of ion clusters:9 (Memory usage:239MB)
2021-11-17 15:45:09,502 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_854_857_PeakCluster.serFS...
2021-11-17 15:45:09,503 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:09,660 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:09,913 INFO  [root] ==================================================================================
2021-11-17 15:45:09,913 INFO  [root] Processing DIA MS2 (mz range):851.0_854.0( 43/61 )
2021-11-17 15:45:09,948 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:09,948 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:10,445 INFO  [root] 85623 Peak curves found (Memory usage:234MB)
2021-11-17 15:45:10,446 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:10,446 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:10,836 INFO  [root] No of ion clusters:11 (Memory usage:240MB)
2021-11-17 15:45:10,836 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_851_854_PeakCluster.serFS...
2021-11-17 15:45:10,837 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:10,957 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:11,198 INFO  [root] ==================================================================================
2021-11-17 15:45:11,198 INFO  [root] Processing DIA MS2 (mz range):848.0_851.0( 44/61 )
2021-11-17 15:45:11,233 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:11,233 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:11,737 INFO  [root] 87198 Peak curves found (Memory usage:235MB)
2021-11-17 15:45:11,739 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:11,739 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:12,110 INFO  [root] No of ion clusters:8 (Memory usage:241MB)
2021-11-17 15:45:12,111 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_848_851_PeakCluster.serFS...
2021-11-17 15:45:12,111 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:12,304 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:12,543 INFO  [root] ==================================================================================
2021-11-17 15:45:12,543 INFO  [root] Processing DIA MS2 (mz range):845.0_848.0( 45/61 )
2021-11-17 15:45:12,578 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:12,578 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:13,028 INFO  [root] 86188 Peak curves found (Memory usage:235MB)
2021-11-17 15:45:13,029 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:13,029 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:13,385 INFO  [root] No of ion clusters:10 (Memory usage:241MB)
2021-11-17 15:45:13,385 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_845_848_PeakCluster.serFS...
2021-11-17 15:45:13,386 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:13,515 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:13,769 INFO  [root] ==================================================================================
2021-11-17 15:45:13,770 INFO  [root] Processing DIA MS2 (mz range):842.0_845.0( 46/61 )
2021-11-17 15:45:13,804 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:13,804 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:14,297 INFO  [root] 85882 Peak curves found (Memory usage:234MB)
2021-11-17 15:45:14,299 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:14,299 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:14,696 INFO  [root] No of ion clusters:10 (Memory usage:240MB)
2021-11-17 15:45:14,697 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_842_845_PeakCluster.serFS...
2021-11-17 15:45:14,697 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:14,825 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:15,059 INFO  [root] ==================================================================================
2021-11-17 15:45:15,059 INFO  [root] Processing DIA MS2 (mz range):839.0_842.0( 47/61 )
2021-11-17 15:45:15,093 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:15,093 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:15,557 INFO  [root] 85065 Peak curves found (Memory usage:235MB)
2021-11-17 15:45:15,559 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:15,559 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:15,889 INFO  [root] No of ion clusters:7 (Memory usage:241MB)
2021-11-17 15:45:15,889 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_839_842_PeakCluster.serFS...
2021-11-17 15:45:15,890 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:16,086 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:16,338 INFO  [root] ==================================================================================
2021-11-17 15:45:16,338 INFO  [root] Processing DIA MS2 (mz range):836.0_839.0( 48/61 )
2021-11-17 15:45:16,373 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:16,373 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:16,813 INFO  [root] 90077 Peak curves found (Memory usage:236MB)
2021-11-17 15:45:16,815 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:16,815 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:17,154 INFO  [root] No of ion clusters:9 (Memory usage:243MB)
2021-11-17 15:45:17,155 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_836_839_PeakCluster.serFS...
2021-11-17 15:45:17,155 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:17,328 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:17,572 INFO  [root] ==================================================================================
2021-11-17 15:45:17,573 INFO  [root] Processing DIA MS2 (mz range):833.0_836.0( 49/61 )
2021-11-17 15:45:17,605 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:17,605 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:18,163 INFO  [root] 93363 Peak curves found (Memory usage:238MB)
2021-11-17 15:45:18,165 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:18,165 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:18,516 INFO  [root] No of ion clusters:10 (Memory usage:245MB)
2021-11-17 15:45:18,516 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_833_836_PeakCluster.serFS...
2021-11-17 15:45:18,516 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:18,678 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:18,927 INFO  [root] ==================================================================================
2021-11-17 15:45:18,927 INFO  [root] Processing DIA MS2 (mz range):830.0_833.0( 50/61 )
2021-11-17 15:45:18,976 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:18,976 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:19,596 INFO  [root] 98369 Peak curves found (Memory usage:240MB)
2021-11-17 15:45:19,598 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:19,598 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:20,034 INFO  [root] No of ion clusters:5 (Memory usage:247MB)
2021-11-17 15:45:20,034 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_830_833_PeakCluster.serFS...
2021-11-17 15:45:20,035 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:20,207 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:20,453 INFO  [root] ==================================================================================
2021-11-17 15:45:20,453 INFO  [root] Processing DIA MS2 (mz range):827.0_830.0( 51/61 )
2021-11-17 15:45:20,488 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:20,488 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:21,012 INFO  [root] 104588 Peak curves found (Memory usage:243MB)
2021-11-17 15:45:21,014 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:21,014 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:21,431 INFO  [root] No of ion clusters:11 (Memory usage:251MB)
2021-11-17 15:45:21,431 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_827_830_PeakCluster.serFS...
2021-11-17 15:45:21,432 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:21,628 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:21,878 INFO  [root] ==================================================================================
2021-11-17 15:45:21,878 INFO  [root] Processing DIA MS2 (mz range):824.0_827.0( 52/61 )
2021-11-17 15:45:21,915 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:21,915 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:22,513 INFO  [root] 111117 Peak curves found (Memory usage:246MB)
2021-11-17 15:45:22,515 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:22,515 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:22,882 INFO  [root] No of ion clusters:8 (Memory usage:255MB)
2021-11-17 15:45:22,882 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_824_827_PeakCluster.serFS...
2021-11-17 15:45:22,882 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:23,080 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:23,323 INFO  [root] ==================================================================================
2021-11-17 15:45:23,323 INFO  [root] Processing DIA MS2 (mz range):821.0_824.0( 53/61 )
2021-11-17 15:45:23,368 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:23,368 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:24,014 INFO  [root] 130447 Peak curves found (Memory usage:256MB)
2021-11-17 15:45:24,016 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:24,016 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:24,510 INFO  [root] No of ion clusters:11 (Memory usage:265MB)
2021-11-17 15:45:24,510 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_821_824_PeakCluster.serFS...
2021-11-17 15:45:24,511 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:24,741 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:25,005 INFO  [root] ==================================================================================
2021-11-17 15:45:25,006 INFO  [root] Processing DIA MS2 (mz range):818.0_821.0( 54/61 )
2021-11-17 15:45:25,059 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:25,059 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:25,810 INFO  [root] 131005 Peak curves found (Memory usage:256MB)
2021-11-17 15:45:25,812 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:25,812 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:26,218 INFO  [root] No of ion clusters:12 (Memory usage:267MB)
2021-11-17 15:45:26,218 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_818_821_PeakCluster.serFS...
2021-11-17 15:45:26,218 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:26,443 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:26,721 INFO  [root] ==================================================================================
2021-11-17 15:45:26,721 INFO  [root] Processing DIA MS2 (mz range):815.0_818.0( 55/61 )
2021-11-17 15:45:26,763 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:26,763 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:27,338 INFO  [root] 118050 Peak curves found (Memory usage:251MB)
2021-11-17 15:45:27,340 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:27,340 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:27,758 INFO  [root] No of ion clusters:9 (Memory usage:260MB)
2021-11-17 15:45:27,758 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_815_818_PeakCluster.serFS...
2021-11-17 15:45:27,759 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:27,987 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:28,244 INFO  [root] ==================================================================================
2021-11-17 15:45:28,244 INFO  [root] Processing DIA MS2 (mz range):812.0_815.0( 56/61 )
2021-11-17 15:45:28,280 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:28,281 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:28,819 INFO  [root] 103697 Peak curves found (Memory usage:246MB)
2021-11-17 15:45:28,820 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:28,820 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:29,196 INFO  [root] No of ion clusters:10 (Memory usage:253MB)
2021-11-17 15:45:29,196 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_812_815_PeakCluster.serFS...
2021-11-17 15:45:29,197 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:29,387 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:29,650 INFO  [root] ==================================================================================
2021-11-17 15:45:29,650 INFO  [root] Processing DIA MS2 (mz range):809.0_812.0( 57/61 )
2021-11-17 15:45:29,686 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:29,686 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:30,193 INFO  [root] 100816 Peak curves found (Memory usage:245MB)
2021-11-17 15:45:30,194 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:30,194 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:30,565 INFO  [root] No of ion clusters:16 (Memory usage:253MB)
2021-11-17 15:45:30,565 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_809_812_PeakCluster.serFS...
2021-11-17 15:45:30,566 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:30,827 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:31,130 INFO  [root] ==================================================================================
2021-11-17 15:45:31,130 INFO  [root] Processing DIA MS2 (mz range):806.0_809.0( 58/61 )
2021-11-17 15:45:31,174 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:31,174 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:31,749 INFO  [root] 103378 Peak curves found (Memory usage:246MB)
2021-11-17 15:45:31,751 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:31,751 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:32,114 INFO  [root] No of ion clusters:11 (Memory usage:254MB)
2021-11-17 15:45:32,114 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_806_809_PeakCluster.serFS...
2021-11-17 15:45:32,115 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:32,353 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:32,610 INFO  [root] ==================================================================================
2021-11-17 15:45:32,611 INFO  [root] Processing DIA MS2 (mz range):803.0_806.0( 59/61 )
2021-11-17 15:45:32,667 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:32,667 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:33,268 INFO  [root] 93439 Peak curves found (Memory usage:243MB)
2021-11-17 15:45:33,271 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:33,271 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:33,685 INFO  [root] No of ion clusters:7 (Memory usage:250MB)
2021-11-17 15:45:33,685 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_803_806_PeakCluster.serFS...
2021-11-17 15:45:33,685 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:33,941 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:34,215 INFO  [root] ==================================================================================
2021-11-17 15:45:34,215 INFO  [root] Processing DIA MS2 (mz range):800.0_803.0( 60/61 )
2021-11-17 15:45:34,246 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:34,247 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:34,712 INFO  [root] 57121 Peak curves found (Memory usage:229MB)
2021-11-17 15:45:34,714 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:34,714 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:35,013 INFO  [root] No of ion clusters:14 (Memory usage:233MB)
2021-11-17 15:45:35,013 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_800_803_PeakCluster.serFS...
2021-11-17 15:45:35,014 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:35,193 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:35,482 INFO  [root] ==================================================================================
2021-11-17 15:45:35,482 INFO  [root] Processing DIA MS2 (mz range):797.0_800.0( 61/61 )
2021-11-17 15:45:35,504 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:35,504 INFO  [root] Smoothing detected signals......
2021-11-17 15:45:36,499 INFO  [root] 53633 Peak curves found (Memory usage:231MB)
2021-11-17 15:45:36,501 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:45:36,501 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:45:36,828 INFO  [root] No of ion clusters:58 (Memory usage:235MB)
2021-11-17 15:45:36,828 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_797_800_PeakCluster.serFS...
2021-11-17 15:45:36,829 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:45:37,391 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:45:37,868 INFO  [root] ==================================================================================
2021-11-17 15:45:39,397 INFO  [root] C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.mzXML processed time:0 hour, 1 min, 47 sec
2021-11-17 15:45:39,397 INFO  [root] Job complete
2021-11-17 15:45:39,397 INFO  [root] =================================================================================================
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
=================================================================================================
DIA-Umpire singal extraction analysis  (version: v2.2.3)
(c) University of Michigan
2021-11-17 15:45:46,857 INFO  [root] Version: v2.2.3
2021-11-17 15:45:46,857 INFO  [root] Parameter file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
2021-11-17 15:45:46,858 INFO  [root] Spectra file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.mzXML
2021-11-17 15:45:46,860 INFO  [root] 
2021-11-17 15:45:46,860 INFO  [root] ####################################################################################################
2021-11-17 15:45:46,860 INFO  [root] #No of threads
2021-11-17 15:45:46,860 INFO  [root] Thread = 7
2021-11-17 15:45:46,860 INFO  [root] ####################################################################################################
2021-11-17 15:45:46,860 INFO  [root] 
2021-11-17 15:45:46,860 INFO  [root] ## omit Thread
2021-11-17 15:45:46,860 INFO  [root] 
2021-11-17 15:45:46,860 INFO  [root] #Precursor-fragments grouping parameters
2021-11-17 15:45:46,860 INFO  [root] RPmax = 25
2021-11-17 15:45:46,861 INFO  [root] RFmax = 500
2021-11-17 15:45:46,861 INFO  [root] CorrThreshold = 0
2021-11-17 15:45:46,861 INFO  [root] DeltaApex = 0.2
2021-11-17 15:45:46,862 INFO  [root] RTOverlap = 0.3
2021-11-17 15:45:46,862 INFO  [root] 
2021-11-17 15:45:46,862 INFO  [root] #Fragment intensity adjustments
2021-11-17 15:45:46,862 INFO  [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2021-11-17 15:45:46,862 INFO  [root] AdjustFragIntensity = true
2021-11-17 15:45:46,862 INFO  [root] BoostComplementaryIon = false
2021-11-17 15:45:46,862 INFO  [root] 
2021-11-17 15:45:46,862 INFO  [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2021-11-17 15:45:46,862 INFO  [root] ExportPrecursorPeak = false
2021-11-17 15:45:46,862 INFO  [root] 
2021-11-17 15:45:46,862 INFO  [root] Q1 = true
2021-11-17 15:45:46,862 INFO  [root] Q2 = true
2021-11-17 15:45:46,862 INFO  [root] Q3 = true
2021-11-17 15:45:46,862 INFO  [root] 
2021-11-17 15:45:46,862 INFO  [root] #Signal extraction: mass accuracy and resolution
2021-11-17 15:45:46,862 INFO  [root] # resolution parameter matters only for data generated in profile mode
2021-11-17 15:45:46,862 INFO  [root] SE.MS1PPM = 10
2021-11-17 15:45:46,862 INFO  [root] SE.MS2PPM = 10
2021-11-17 15:45:46,863 INFO  [root] SE.Resolution = 60000
2021-11-17 15:45:46,863 INFO  [root] 
2021-11-17 15:45:46,863 INFO  [root] #Signal extraction: signal to noise filter
2021-11-17 15:45:46,863 INFO  [root] SE.SN = 1.1
2021-11-17 15:45:46,863 INFO  [root] SE.MS2SN = 1.1
2021-11-17 15:45:46,863 INFO  [root] 
2021-11-17 15:45:46,863 INFO  [root] #Signal extraction: minimum signal intensity filter
2021-11-17 15:45:46,863 INFO  [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2021-11-17 15:45:46,863 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2021-11-17 15:45:46,863 INFO  [root] SE.EstimateBG = false
2021-11-17 15:45:46,863 INFO  [root] SE.MinMSIntensity = 1
2021-11-17 15:45:46,863 INFO  [root] SE.MinMSMSIntensity = 1
2021-11-17 15:45:46,863 INFO  [root] 
2021-11-17 15:45:46,863 INFO  [root] #Signal extraction: peak curve detection and isotope grouping
2021-11-17 15:45:46,863 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2021-11-17 15:45:46,863 INFO  [root] SE.NoMissedScan = 1
2021-11-17 15:45:46,864 INFO  [root] SE.MaxCurveRTRange = 2
2021-11-17 15:45:46,864 INFO  [root] SE.RemoveGroupedPeaks = true
2021-11-17 15:45:46,864 INFO  [root] SE.RemoveGroupedPeaksRTOverlap = 0.3
2021-11-17 15:45:46,868 INFO  [root] SE.RemoveGroupedPeaksCorr = 0.3
2021-11-17 15:45:46,868 INFO  [root] SE.MinNoPeakCluster = 2
2021-11-17 15:45:46,868 INFO  [root] SE.MaxNoPeakCluster = 4
2021-11-17 15:45:46,868 INFO  [root] 
2021-11-17 15:45:46,868 INFO  [root] #Signal extraction: filtering of MS1 features
2021-11-17 15:45:46,868 INFO  [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2021-11-17 15:45:46,868 INFO  [root] SE.IsoPattern = 0.3
2021-11-17 15:45:46,868 INFO  [root] SE.MassDefectFilter = false
2021-11-17 15:45:46,868 INFO  [root] SE.MassDefectOffset = 0.1
2021-11-17 15:45:46,868 INFO  [root] 
2021-11-17 15:45:46,869 INFO  [root] #Signal extraction: other
2021-11-17 15:45:46,869 INFO  [root] SE.StartCharge = 1
2021-11-17 15:45:46,869 INFO  [root] SE.EndCharge = 5
2021-11-17 15:45:46,869 INFO  [root] SE.MS2StartCharge = 2
2021-11-17 15:45:46,869 INFO  [root] SE.MS2EndCharge = 5
2021-11-17 15:45:46,869 INFO  [root] SE.MinFrag = 10
2021-11-17 15:45:46,869 INFO  [root] SE.StartRT = 0
2021-11-17 15:45:46,869 INFO  [root] SE.EndRT = 9999
2021-11-17 15:45:46,869 INFO  [root] SE.MinMZ = 200
2021-11-17 15:45:46,869 INFO  [root] SE.MinPrecursorMass = 600
2021-11-17 15:45:46,869 INFO  [root] SE.MaxPrecursorMass = 5000
2021-11-17 15:45:46,869 INFO  [root] 
2021-11-17 15:45:46,869 INFO  [root] 
2021-11-17 15:45:46,869 INFO  [root] #Isolation window setting
2021-11-17 15:45:46,869 INFO  [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2021-11-17 15:45:46,869 INFO  [root] WindowType = SWATH
2021-11-17 15:45:46,869 INFO  [root] 
2021-11-17 15:45:46,869 INFO  [root] #Fix window size (For SWATH)
2021-11-17 15:45:46,869 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:45:46,869 INFO  [root] WindowSize = 10
2021-11-17 15:45:46,869 INFO  [root] 
2021-11-17 15:45:46,869 INFO  [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2021-11-17 15:45:46,869 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:45:46,870 INFO  [root] ==window setting begin
2021-11-17 15:45:46,870 INFO  [root] 
2021-11-17 15:45:46,870 INFO  [root] =================================================================================================
2021-11-17 15:45:46,870 INFO  [root] Processing C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.mzXML....
2021-11-17 15:45:46,873 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_diasetting.ser...
2021-11-17 15:45:46,882 INFO  [root] Writing parameter to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_params.ser...
2021-11-17 15:45:46,883 INFO  [root] Module A: Signal extraction
2021-11-17 15:45:52,004 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_diasetting.ser...
2021-11-17 15:45:52,544 INFO  [root] Processing MS1 peak detection
2021-11-17 15:45:52,546 INFO  [root] MS1 average cycle time : 2.671036 seconds
2021-11-17 15:45:57,897 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:45:57,898 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:03,731 INFO  [root] 402421 Peak curves found (Memory usage:385MB)
2021-11-17 15:46:03,731 INFO  [root] Inclusion mz values found: 0/0
2021-11-17 15:46:03,731 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:03,732 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:16,384 INFO  [root] No of ion clusters:33440 (Memory usage:236MB)
2021-11-17 15:46:16,404 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_PeakCluster.serFS...
2021-11-17 15:46:16,721 INFO  [root] ==================================================================================
2021-11-17 15:46:16,721 INFO  [root] Processing DIA MS2 (mz range):977.0_980.0( 1/61 )
2021-11-17 15:46:16,825 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:16,825 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:18,195 INFO  [root] 95033 Peak curves found (Memory usage:297MB)
2021-11-17 15:46:18,200 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:18,200 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:18,672 INFO  [root] No of ion clusters:48 (Memory usage:304MB)
2021-11-17 15:46:18,672 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_977_980_PeakCluster.serFS...
2021-11-17 15:46:18,674 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:20,068 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:20,990 INFO  [root] ==================================================================================
2021-11-17 15:46:20,990 INFO  [root] Processing DIA MS2 (mz range):974.0_977.0( 2/61 )
2021-11-17 15:46:21,084 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:21,084 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:22,481 INFO  [root] 114244 Peak curves found (Memory usage:291MB)
2021-11-17 15:46:22,483 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:22,483 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:22,960 INFO  [root] No of ion clusters:16 (Memory usage:299MB)
2021-11-17 15:46:22,960 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_974_977_PeakCluster.serFS...
2021-11-17 15:46:22,961 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:23,559 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:23,998 INFO  [root] ==================================================================================
2021-11-17 15:46:23,998 INFO  [root] Processing DIA MS2 (mz range):971.0_974.0( 3/61 )
2021-11-17 15:46:24,100 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:24,100 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:25,856 INFO  [root] 180615 Peak curves found (Memory usage:319MB)
2021-11-17 15:46:25,858 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:25,858 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:26,489 INFO  [root] No of ion clusters:18 (Memory usage:333MB)
2021-11-17 15:46:26,489 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_971_974_PeakCluster.serFS...
2021-11-17 15:46:26,490 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:27,211 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:27,636 INFO  [root] ==================================================================================
2021-11-17 15:46:27,636 INFO  [root] Processing DIA MS2 (mz range):968.0_971.0( 4/61 )
2021-11-17 15:46:27,695 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:27,695 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:28,671 INFO  [root] 182690 Peak curves found (Memory usage:319MB)
2021-11-17 15:46:28,673 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:28,673 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:29,256 INFO  [root] No of ion clusters:25 (Memory usage:332MB)
2021-11-17 15:46:29,256 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_968_971_PeakCluster.serFS...
2021-11-17 15:46:29,257 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:29,932 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:30,399 INFO  [root] ==================================================================================
2021-11-17 15:46:30,399 INFO  [root] Processing DIA MS2 (mz range):965.0_968.0( 5/61 )
2021-11-17 15:46:30,471 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:30,471 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:31,724 INFO  [root] 196770 Peak curves found (Memory usage:325MB)
2021-11-17 15:46:31,726 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:31,726 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:32,430 INFO  [root] No of ion clusters:13 (Memory usage:341MB)
2021-11-17 15:46:32,430 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_965_968_PeakCluster.serFS...
2021-11-17 15:46:32,431 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:33,191 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:33,559 INFO  [root] ==================================================================================
2021-11-17 15:46:33,559 INFO  [root] Processing DIA MS2 (mz range):962.0_965.0( 6/61 )
2021-11-17 15:46:33,643 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:33,643 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:35,193 INFO  [root] 237504 Peak curves found (Memory usage:344MB)
2021-11-17 15:46:35,197 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:35,197 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:35,911 INFO  [root] No of ion clusters:26 (Memory usage:362MB)
2021-11-17 15:46:35,911 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_962_965_PeakCluster.serFS...
2021-11-17 15:46:35,912 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:36,588 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:36,997 INFO  [root] ==================================================================================
2021-11-17 15:46:36,997 INFO  [root] Processing DIA MS2 (mz range):959.0_962.0( 7/61 )
2021-11-17 15:46:37,083 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:37,083 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:39,394 INFO  [root] 231373 Peak curves found (Memory usage:346MB)
2021-11-17 15:46:39,396 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:39,396 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:40,108 INFO  [root] No of ion clusters:13 (Memory usage:364MB)
2021-11-17 15:46:40,108 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_959_962_PeakCluster.serFS...
2021-11-17 15:46:40,109 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:41,018 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:41,390 INFO  [root] ==================================================================================
2021-11-17 15:46:41,391 INFO  [root] Processing DIA MS2 (mz range):956.0_959.0( 8/61 )
2021-11-17 15:46:41,461 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:41,461 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:42,819 INFO  [root] 248461 Peak curves found (Memory usage:351MB)
2021-11-17 15:46:42,821 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:42,821 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:43,642 INFO  [root] No of ion clusters:17 (Memory usage:370MB)
2021-11-17 15:46:43,642 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_956_959_PeakCluster.serFS...
2021-11-17 15:46:43,643 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:44,348 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:44,706 INFO  [root] ==================================================================================
2021-11-17 15:46:44,706 INFO  [root] Processing DIA MS2 (mz range):953.0_956.0( 9/61 )
2021-11-17 15:46:44,789 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:44,789 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:48,091 INFO  [root] 209291 Peak curves found (Memory usage:338MB)
2021-11-17 15:46:48,093 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:48,093 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:48,788 INFO  [root] No of ion clusters:28 (Memory usage:355MB)
2021-11-17 15:46:48,788 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_953_956_PeakCluster.serFS...
2021-11-17 15:46:48,789 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:49,406 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:49,787 INFO  [root] ==================================================================================
2021-11-17 15:46:49,787 INFO  [root] Processing DIA MS2 (mz range):950.0_953.0( 10/61 )
2021-11-17 15:46:49,858 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:49,858 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:51,522 INFO  [root] 223594 Peak curves found (Memory usage:344MB)
2021-11-17 15:46:51,524 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:51,524 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:52,362 INFO  [root] No of ion clusters:23 (Memory usage:361MB)
2021-11-17 15:46:52,363 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_950_953_PeakCluster.serFS...
2021-11-17 15:46:52,364 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:52,917 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:53,342 INFO  [root] ==================================================================================
2021-11-17 15:46:53,342 INFO  [root] Processing DIA MS2 (mz range):947.0_950.0( 11/61 )
2021-11-17 15:46:53,428 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:53,428 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:54,871 INFO  [root] 220812 Peak curves found (Memory usage:345MB)
2021-11-17 15:46:54,872 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:54,872 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:55,625 INFO  [root] No of ion clusters:39 (Memory usage:362MB)
2021-11-17 15:46:55,625 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_947_950_PeakCluster.serFS...
2021-11-17 15:46:55,626 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:56,373 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:46:56,832 INFO  [root] ==================================================================================
2021-11-17 15:46:56,832 INFO  [root] Processing DIA MS2 (mz range):944.0_947.0( 12/61 )
2021-11-17 15:46:56,908 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:46:56,908 INFO  [root] Smoothing detected signals......
2021-11-17 15:46:58,451 INFO  [root] 220817 Peak curves found (Memory usage:347MB)
2021-11-17 15:46:58,452 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:46:58,452 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:46:59,166 INFO  [root] No of ion clusters:37 (Memory usage:364MB)
2021-11-17 15:46:59,166 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_944_947_PeakCluster.serFS...
2021-11-17 15:46:59,167 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:46:59,866 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:00,324 INFO  [root] ==================================================================================
2021-11-17 15:47:00,324 INFO  [root] Processing DIA MS2 (mz range):941.0_944.0( 13/61 )
2021-11-17 15:47:00,413 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:00,413 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:01,906 INFO  [root] 214569 Peak curves found (Memory usage:345MB)
2021-11-17 15:47:01,909 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:01,909 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:02,626 INFO  [root] No of ion clusters:16 (Memory usage:361MB)
2021-11-17 15:47:02,626 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_941_944_PeakCluster.serFS...
2021-11-17 15:47:02,627 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:03,230 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:03,673 INFO  [root] ==================================================================================
2021-11-17 15:47:03,673 INFO  [root] Processing DIA MS2 (mz range):938.0_941.0( 14/61 )
2021-11-17 15:47:03,760 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:03,760 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:06,574 INFO  [root] 236572 Peak curves found (Memory usage:356MB)
2021-11-17 15:47:06,576 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:06,576 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:07,392 INFO  [root] No of ion clusters:27 (Memory usage:374MB)
2021-11-17 15:47:07,392 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_938_941_PeakCluster.serFS...
2021-11-17 15:47:07,393 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:07,900 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:08,335 INFO  [root] ==================================================================================
2021-11-17 15:47:08,335 INFO  [root] Processing DIA MS2 (mz range):935.0_938.0( 15/61 )
2021-11-17 15:47:08,433 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:08,433 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:11,555 INFO  [root] 220114 Peak curves found (Memory usage:353MB)
2021-11-17 15:47:11,556 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:11,556 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:12,300 INFO  [root] No of ion clusters:18 (Memory usage:371MB)
2021-11-17 15:47:12,300 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_935_938_PeakCluster.serFS...
2021-11-17 15:47:12,301 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:12,991 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:13,388 INFO  [root] ==================================================================================
2021-11-17 15:47:13,388 INFO  [root] Processing DIA MS2 (mz range):932.0_935.0( 16/61 )
2021-11-17 15:47:13,451 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:13,451 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:14,509 INFO  [root] 200750 Peak curves found (Memory usage:342MB)
2021-11-17 15:47:14,510 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:14,510 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:15,243 INFO  [root] No of ion clusters:17 (Memory usage:356MB)
2021-11-17 15:47:15,243 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_932_935_PeakCluster.serFS...
2021-11-17 15:47:15,243 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:15,640 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:16,006 INFO  [root] ==================================================================================
2021-11-17 15:47:16,006 INFO  [root] Processing DIA MS2 (mz range):929.0_932.0( 17/61 )
2021-11-17 15:47:16,062 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:16,062 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:17,313 INFO  [root] 173191 Peak curves found (Memory usage:332MB)
2021-11-17 15:47:17,315 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:17,315 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:17,947 INFO  [root] No of ion clusters:19 (Memory usage:346MB)
2021-11-17 15:47:17,947 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_929_932_PeakCluster.serFS...
2021-11-17 15:47:17,948 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:18,592 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:18,967 INFO  [root] ==================================================================================
2021-11-17 15:47:18,967 INFO  [root] Processing DIA MS2 (mz range):926.0_929.0( 18/61 )
2021-11-17 15:47:19,026 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:19,026 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:19,967 INFO  [root] 172147 Peak curves found (Memory usage:333MB)
2021-11-17 15:47:19,969 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:19,969 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:20,557 INFO  [root] No of ion clusters:25 (Memory usage:346MB)
2021-11-17 15:47:20,558 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_926_929_PeakCluster.serFS...
2021-11-17 15:47:20,558 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:21,183 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:21,593 INFO  [root] ==================================================================================
2021-11-17 15:47:21,593 INFO  [root] Processing DIA MS2 (mz range):923.0_926.0( 19/61 )
2021-11-17 15:47:21,647 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:21,647 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:22,543 INFO  [root] 161597 Peak curves found (Memory usage:329MB)
2021-11-17 15:47:22,545 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:22,545 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:23,192 INFO  [root] No of ion clusters:22 (Memory usage:341MB)
2021-11-17 15:47:23,192 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_923_926_PeakCluster.serFS...
2021-11-17 15:47:23,192 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:23,682 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:24,053 INFO  [root] ==================================================================================
2021-11-17 15:47:24,053 INFO  [root] Processing DIA MS2 (mz range):920.0_923.0( 20/61 )
2021-11-17 15:47:24,111 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:24,111 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:25,022 INFO  [root] 179333 Peak curves found (Memory usage:336MB)
2021-11-17 15:47:25,025 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:25,025 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:25,651 INFO  [root] No of ion clusters:18 (Memory usage:349MB)
2021-11-17 15:47:25,651 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_920_923_PeakCluster.serFS...
2021-11-17 15:47:25,652 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:26,062 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:26,424 INFO  [root] ==================================================================================
2021-11-17 15:47:26,424 INFO  [root] Processing DIA MS2 (mz range):917.0_920.0( 21/61 )
2021-11-17 15:47:26,488 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:26,488 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:28,062 INFO  [root] 169533 Peak curves found (Memory usage:334MB)
2021-11-17 15:47:28,063 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:28,064 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:28,639 INFO  [root] No of ion clusters:20 (Memory usage:347MB)
2021-11-17 15:47:28,639 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_917_920_PeakCluster.serFS...
2021-11-17 15:47:28,639 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:29,180 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:29,536 INFO  [root] ==================================================================================
2021-11-17 15:47:29,536 INFO  [root] Processing DIA MS2 (mz range):914.0_917.0( 22/61 )
2021-11-17 15:47:29,599 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:29,599 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:30,757 INFO  [root] 186901 Peak curves found (Memory usage:339MB)
2021-11-17 15:47:30,758 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:30,758 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:31,427 INFO  [root] No of ion clusters:22 (Memory usage:354MB)
2021-11-17 15:47:31,427 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_914_917_PeakCluster.serFS...
2021-11-17 15:47:31,429 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:31,901 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:32,251 INFO  [root] ==================================================================================
2021-11-17 15:47:32,251 INFO  [root] Processing DIA MS2 (mz range):911.0_914.0( 23/61 )
2021-11-17 15:47:32,310 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:32,310 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:33,401 INFO  [root] 180192 Peak curves found (Memory usage:338MB)
2021-11-17 15:47:33,403 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:33,403 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:34,014 INFO  [root] No of ion clusters:27 (Memory usage:352MB)
2021-11-17 15:47:34,014 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_911_914_PeakCluster.serFS...
2021-11-17 15:47:34,015 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:34,730 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:35,159 INFO  [root] ==================================================================================
2021-11-17 15:47:35,159 INFO  [root] Processing DIA MS2 (mz range):908.0_911.0( 24/61 )
2021-11-17 15:47:35,243 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:35,243 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:36,419 INFO  [root] 177394 Peak curves found (Memory usage:337MB)
2021-11-17 15:47:36,421 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:36,421 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:37,014 INFO  [root] No of ion clusters:26 (Memory usage:350MB)
2021-11-17 15:47:37,014 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_908_911_PeakCluster.serFS...
2021-11-17 15:47:37,015 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:37,528 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:37,904 INFO  [root] ==================================================================================
2021-11-17 15:47:37,904 INFO  [root] Processing DIA MS2 (mz range):905.0_908.0( 25/61 )
2021-11-17 15:47:37,965 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:37,965 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:39,026 INFO  [root] 162929 Peak curves found (Memory usage:331MB)
2021-11-17 15:47:39,027 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:39,027 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:39,594 INFO  [root] No of ion clusters:22 (Memory usage:343MB)
2021-11-17 15:47:39,594 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_905_908_PeakCluster.serFS...
2021-11-17 15:47:39,595 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:40,172 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:40,554 INFO  [root] ==================================================================================
2021-11-17 15:47:40,554 INFO  [root] Processing DIA MS2 (mz range):902.0_905.0( 26/61 )
2021-11-17 15:47:40,615 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:40,615 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:41,493 INFO  [root] 150501 Peak curves found (Memory usage:326MB)
2021-11-17 15:47:41,495 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:41,495 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:42,069 INFO  [root] No of ion clusters:25 (Memory usage:337MB)
2021-11-17 15:47:42,069 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_902_905_PeakCluster.serFS...
2021-11-17 15:47:42,070 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:42,459 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:42,833 INFO  [root] ==================================================================================
2021-11-17 15:47:42,834 INFO  [root] Processing DIA MS2 (mz range):899.0_902.0( 27/61 )
2021-11-17 15:47:42,886 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:42,886 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:43,794 INFO  [root] 164267 Peak curves found (Memory usage:333MB)
2021-11-17 15:47:43,795 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:43,795 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:44,361 INFO  [root] No of ion clusters:12 (Memory usage:345MB)
2021-11-17 15:47:44,361 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_899_902_PeakCluster.serFS...
2021-11-17 15:47:44,362 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:44,776 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:45,118 INFO  [root] ==================================================================================
2021-11-17 15:47:45,118 INFO  [root] Processing DIA MS2 (mz range):896.0_899.0( 28/61 )
2021-11-17 15:47:45,184 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:45,184 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:46,612 INFO  [root] 191545 Peak curves found (Memory usage:345MB)
2021-11-17 15:47:46,614 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:46,614 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:47,279 INFO  [root] No of ion clusters:25 (Memory usage:360MB)
2021-11-17 15:47:47,279 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_896_899_PeakCluster.serFS...
2021-11-17 15:47:47,280 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:48,006 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:48,425 INFO  [root] ==================================================================================
2021-11-17 15:47:48,425 INFO  [root] Processing DIA MS2 (mz range):893.0_896.0( 29/61 )
2021-11-17 15:47:48,507 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:48,507 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:49,909 INFO  [root] 198917 Peak curves found (Memory usage:348MB)
2021-11-17 15:47:49,911 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:49,911 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:50,624 INFO  [root] No of ion clusters:29 (Memory usage:363MB)
2021-11-17 15:47:50,624 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_893_896_PeakCluster.serFS...
2021-11-17 15:47:50,625 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:51,391 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:51,846 INFO  [root] ==================================================================================
2021-11-17 15:47:51,846 INFO  [root] Processing DIA MS2 (mz range):890.0_893.0( 30/61 )
2021-11-17 15:47:51,916 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:51,917 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:52,966 INFO  [root] 191119 Peak curves found (Memory usage:344MB)
2021-11-17 15:47:52,968 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:52,968 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:53,667 INFO  [root] No of ion clusters:24 (Memory usage:359MB)
2021-11-17 15:47:53,667 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_890_893_PeakCluster.serFS...
2021-11-17 15:47:53,668 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:54,236 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:54,626 INFO  [root] ==================================================================================
2021-11-17 15:47:54,626 INFO  [root] Processing DIA MS2 (mz range):887.0_890.0( 31/61 )
2021-11-17 15:47:54,689 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:54,689 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:55,728 INFO  [root] 182067 Peak curves found (Memory usage:341MB)
2021-11-17 15:47:55,730 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:55,730 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:56,388 INFO  [root] No of ion clusters:23 (Memory usage:355MB)
2021-11-17 15:47:56,388 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_887_890_PeakCluster.serFS...
2021-11-17 15:47:56,389 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:57,082 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:47:57,479 INFO  [root] ==================================================================================
2021-11-17 15:47:57,479 INFO  [root] Processing DIA MS2 (mz range):884.0_887.0( 32/61 )
2021-11-17 15:47:57,557 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:47:57,557 INFO  [root] Smoothing detected signals......
2021-11-17 15:47:58,580 INFO  [root] 177678 Peak curves found (Memory usage:339MB)
2021-11-17 15:47:58,582 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:47:58,582 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:47:59,221 INFO  [root] No of ion clusters:21 (Memory usage:353MB)
2021-11-17 15:47:59,221 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_884_887_PeakCluster.serFS...
2021-11-17 15:47:59,222 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:47:59,762 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:00,219 INFO  [root] ==================================================================================
2021-11-17 15:48:00,219 INFO  [root] Processing DIA MS2 (mz range):881.0_884.0( 33/61 )
2021-11-17 15:48:00,309 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:00,309 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:01,407 INFO  [root] 161021 Peak curves found (Memory usage:334MB)
2021-11-17 15:48:01,408 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:01,408 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:01,999 INFO  [root] No of ion clusters:15 (Memory usage:347MB)
2021-11-17 15:48:01,999 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_881_884_PeakCluster.serFS...
2021-11-17 15:48:02,000 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:02,497 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:02,856 INFO  [root] ==================================================================================
2021-11-17 15:48:02,856 INFO  [root] Processing DIA MS2 (mz range):878.0_881.0( 34/61 )
2021-11-17 15:48:02,920 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:02,920 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:03,788 INFO  [root] 155103 Peak curves found (Memory usage:331MB)
2021-11-17 15:48:03,789 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:03,789 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:04,406 INFO  [root] No of ion clusters:11 (Memory usage:343MB)
2021-11-17 15:48:04,406 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_878_881_PeakCluster.serFS...
2021-11-17 15:48:04,407 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:04,834 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:05,179 INFO  [root] ==================================================================================
2021-11-17 15:48:05,179 INFO  [root] Processing DIA MS2 (mz range):875.0_878.0( 35/61 )
2021-11-17 15:48:05,232 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:05,232 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:06,166 INFO  [root] 160557 Peak curves found (Memory usage:334MB)
2021-11-17 15:48:06,168 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:06,168 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:06,728 INFO  [root] No of ion clusters:9 (Memory usage:347MB)
2021-11-17 15:48:06,729 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_875_878_PeakCluster.serFS...
2021-11-17 15:48:06,730 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:07,171 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:07,504 INFO  [root] ==================================================================================
2021-11-17 15:48:07,504 INFO  [root] Processing DIA MS2 (mz range):872.0_875.0( 36/61 )
2021-11-17 15:48:07,562 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:07,562 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:08,720 INFO  [root] 159146 Peak curves found (Memory usage:336MB)
2021-11-17 15:48:08,724 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:08,724 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:09,302 INFO  [root] No of ion clusters:17 (Memory usage:348MB)
2021-11-17 15:48:09,302 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_872_875_PeakCluster.serFS...
2021-11-17 15:48:09,302 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:09,886 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:10,277 INFO  [root] ==================================================================================
2021-11-17 15:48:10,277 INFO  [root] Processing DIA MS2 (mz range):869.0_872.0( 37/61 )
2021-11-17 15:48:10,335 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:10,335 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:11,209 INFO  [root] 159921 Peak curves found (Memory usage:334MB)
2021-11-17 15:48:11,211 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:11,211 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:11,772 INFO  [root] No of ion clusters:15 (Memory usage:346MB)
2021-11-17 15:48:11,772 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_869_872_PeakCluster.serFS...
2021-11-17 15:48:11,772 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:12,146 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:12,527 INFO  [root] ==================================================================================
2021-11-17 15:48:12,527 INFO  [root] Processing DIA MS2 (mz range):866.0_869.0( 38/61 )
2021-11-17 15:48:12,580 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:12,580 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:13,389 INFO  [root] 147815 Peak curves found (Memory usage:330MB)
2021-11-17 15:48:13,391 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:13,391 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:13,929 INFO  [root] No of ion clusters:14 (Memory usage:341MB)
2021-11-17 15:48:13,929 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_866_869_PeakCluster.serFS...
2021-11-17 15:48:13,930 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:14,324 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:14,674 INFO  [root] ==================================================================================
2021-11-17 15:48:14,674 INFO  [root] Processing DIA MS2 (mz range):863.0_866.0( 39/61 )
2021-11-17 15:48:14,728 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:14,728 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:15,532 INFO  [root] 158801 Peak curves found (Memory usage:334MB)
2021-11-17 15:48:15,534 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:15,534 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:16,082 INFO  [root] No of ion clusters:19 (Memory usage:347MB)
2021-11-17 15:48:16,083 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_863_866_PeakCluster.serFS...
2021-11-17 15:48:16,083 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:16,444 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:16,796 INFO  [root] ==================================================================================
2021-11-17 15:48:16,796 INFO  [root] Processing DIA MS2 (mz range):860.0_863.0( 40/61 )
2021-11-17 15:48:16,862 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:16,862 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:17,927 INFO  [root] 196288 Peak curves found (Memory usage:350MB)
2021-11-17 15:48:17,928 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:17,928 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:18,571 INFO  [root] No of ion clusters:20 (Memory usage:365MB)
2021-11-17 15:48:18,571 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_860_863_PeakCluster.serFS...
2021-11-17 15:48:18,571 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:19,149 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:19,527 INFO  [root] ==================================================================================
2021-11-17 15:48:19,527 INFO  [root] Processing DIA MS2 (mz range):857.0_860.0( 41/61 )
2021-11-17 15:48:19,600 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:19,600 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:21,331 INFO  [root] 198862 Peak curves found (Memory usage:354MB)
2021-11-17 15:48:21,332 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:21,332 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:21,983 INFO  [root] No of ion clusters:16 (Memory usage:368MB)
2021-11-17 15:48:21,983 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_857_860_PeakCluster.serFS...
2021-11-17 15:48:21,984 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:22,530 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:22,893 INFO  [root] ==================================================================================
2021-11-17 15:48:22,893 INFO  [root] Processing DIA MS2 (mz range):854.0_857.0( 42/61 )
2021-11-17 15:48:22,965 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:22,965 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:24,023 INFO  [root] 192641 Peak curves found (Memory usage:351MB)
2021-11-17 15:48:24,026 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:24,026 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:24,683 INFO  [root] No of ion clusters:13 (Memory usage:366MB)
2021-11-17 15:48:24,683 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_854_857_PeakCluster.serFS...
2021-11-17 15:48:24,684 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:25,223 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:25,610 INFO  [root] ==================================================================================
2021-11-17 15:48:25,610 INFO  [root] Processing DIA MS2 (mz range):851.0_854.0( 43/61 )
2021-11-17 15:48:25,675 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:25,675 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:26,892 INFO  [root] 206956 Peak curves found (Memory usage:357MB)
2021-11-17 15:48:26,895 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:26,895 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:27,604 INFO  [root] No of ion clusters:19 (Memory usage:372MB)
2021-11-17 15:48:27,604 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_851_854_PeakCluster.serFS...
2021-11-17 15:48:27,605 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:28,145 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:28,543 INFO  [root] ==================================================================================
2021-11-17 15:48:28,543 INFO  [root] Processing DIA MS2 (mz range):848.0_851.0( 44/61 )
2021-11-17 15:48:28,629 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:28,629 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:31,016 INFO  [root] 201481 Peak curves found (Memory usage:358MB)
2021-11-17 15:48:31,018 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:31,018 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:31,807 INFO  [root] No of ion clusters:14 (Memory usage:373MB)
2021-11-17 15:48:31,807 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_848_851_PeakCluster.serFS...
2021-11-17 15:48:31,808 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:32,425 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:32,855 INFO  [root] ==================================================================================
2021-11-17 15:48:32,855 INFO  [root] Processing DIA MS2 (mz range):845.0_848.0( 45/61 )
2021-11-17 15:48:32,929 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:32,929 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:34,184 INFO  [root] 202192 Peak curves found (Memory usage:355MB)
2021-11-17 15:48:34,186 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:34,186 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:34,893 INFO  [root] No of ion clusters:16 (Memory usage:371MB)
2021-11-17 15:48:34,893 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_845_848_PeakCluster.serFS...
2021-11-17 15:48:34,893 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:35,429 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:35,824 INFO  [root] ==================================================================================
2021-11-17 15:48:35,825 INFO  [root] Processing DIA MS2 (mz range):842.0_845.0( 46/61 )
2021-11-17 15:48:35,889 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:35,889 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:36,825 INFO  [root] 170554 Peak curves found (Memory usage:343MB)
2021-11-17 15:48:36,826 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:36,826 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:37,459 INFO  [root] No of ion clusters:25 (Memory usage:356MB)
2021-11-17 15:48:37,459 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_842_845_PeakCluster.serFS...
2021-11-17 15:48:37,460 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:37,938 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:38,350 INFO  [root] ==================================================================================
2021-11-17 15:48:38,351 INFO  [root] Processing DIA MS2 (mz range):839.0_842.0( 47/61 )
2021-11-17 15:48:38,416 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:38,416 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:39,493 INFO  [root] 191189 Peak curves found (Memory usage:352MB)
2021-11-17 15:48:39,494 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:39,494 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:40,257 INFO  [root] No of ion clusters:12 (Memory usage:367MB)
2021-11-17 15:48:40,257 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_839_842_PeakCluster.serFS...
2021-11-17 15:48:40,258 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:40,746 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:41,125 INFO  [root] ==================================================================================
2021-11-17 15:48:41,125 INFO  [root] Processing DIA MS2 (mz range):836.0_839.0( 48/61 )
2021-11-17 15:48:41,210 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:41,210 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:42,891 INFO  [root] 202823 Peak curves found (Memory usage:359MB)
2021-11-17 15:48:42,892 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:42,892 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:43,572 INFO  [root] No of ion clusters:11 (Memory usage:373MB)
2021-11-17 15:48:43,572 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_836_839_PeakCluster.serFS...
2021-11-17 15:48:43,573 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:44,353 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:44,755 INFO  [root] ==================================================================================
2021-11-17 15:48:44,755 INFO  [root] Processing DIA MS2 (mz range):833.0_836.0( 49/61 )
2021-11-17 15:48:44,827 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:44,827 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:46,145 INFO  [root] 222385 Peak curves found (Memory usage:365MB)
2021-11-17 15:48:46,148 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:46,148 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:46,845 INFO  [root] No of ion clusters:11 (Memory usage:381MB)
2021-11-17 15:48:46,845 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_833_836_PeakCluster.serFS...
2021-11-17 15:48:46,846 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:47,557 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:47,934 INFO  [root] ==================================================================================
2021-11-17 15:48:47,934 INFO  [root] Processing DIA MS2 (mz range):830.0_833.0( 50/61 )
2021-11-17 15:48:48,015 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:48,015 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:49,679 INFO  [root] 232280 Peak curves found (Memory usage:368MB)
2021-11-17 15:48:49,681 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:49,681 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:50,403 INFO  [root] No of ion clusters:13 (Memory usage:386MB)
2021-11-17 15:48:50,403 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_830_833_PeakCluster.serFS...
2021-11-17 15:48:50,404 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:51,049 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:51,465 INFO  [root] ==================================================================================
2021-11-17 15:48:51,466 INFO  [root] Processing DIA MS2 (mz range):827.0_830.0( 51/61 )
2021-11-17 15:48:51,555 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:51,555 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:53,378 INFO  [root] 243021 Peak curves found (Memory usage:374MB)
2021-11-17 15:48:53,381 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:53,381 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:54,128 INFO  [root] No of ion clusters:19 (Memory usage:393MB)
2021-11-17 15:48:54,128 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_827_830_PeakCluster.serFS...
2021-11-17 15:48:54,130 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:54,890 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:55,344 INFO  [root] ==================================================================================
2021-11-17 15:48:55,344 INFO  [root] Processing DIA MS2 (mz range):824.0_827.0( 52/61 )
2021-11-17 15:48:55,430 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:55,430 INFO  [root] Smoothing detected signals......
2021-11-17 15:48:57,223 INFO  [root] 252182 Peak curves found (Memory usage:377MB)
2021-11-17 15:48:57,225 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:48:57,225 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:48:58,024 INFO  [root] No of ion clusters:16 (Memory usage:397MB)
2021-11-17 15:48:58,024 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_824_827_PeakCluster.serFS...
2021-11-17 15:48:58,025 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:48:58,714 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:48:59,112 INFO  [root] ==================================================================================
2021-11-17 15:48:59,112 INFO  [root] Processing DIA MS2 (mz range):821.0_824.0( 53/61 )
2021-11-17 15:48:59,207 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:48:59,207 INFO  [root] Smoothing detected signals......
2021-11-17 15:49:00,960 INFO  [root] 265922 Peak curves found (Memory usage:384MB)
2021-11-17 15:49:00,962 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:49:00,962 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:49:01,815 INFO  [root] No of ion clusters:40 (Memory usage:405MB)
2021-11-17 15:49:01,815 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_821_824_PeakCluster.serFS...
2021-11-17 15:49:01,816 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:49:02,703 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:49:03,169 INFO  [root] ==================================================================================
2021-11-17 15:49:03,169 INFO  [root] Processing DIA MS2 (mz range):818.0_821.0( 54/61 )
2021-11-17 15:49:03,263 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:49:03,264 INFO  [root] Smoothing detected signals......
2021-11-17 15:49:05,131 INFO  [root] 264824 Peak curves found (Memory usage:384MB)
2021-11-17 15:49:05,133 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:49:05,133 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:49:06,001 INFO  [root] No of ion clusters:15 (Memory usage:405MB)
2021-11-17 15:49:06,002 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_818_821_PeakCluster.serFS...
2021-11-17 15:49:06,002 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:49:07,118 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:49:07,566 INFO  [root] ==================================================================================
2021-11-17 15:49:07,566 INFO  [root] Processing DIA MS2 (mz range):815.0_818.0( 55/61 )
2021-11-17 15:49:07,647 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:49:07,647 INFO  [root] Smoothing detected signals......
2021-11-17 15:49:09,302 INFO  [root] 267940 Peak curves found (Memory usage:385MB)
2021-11-17 15:49:09,304 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:49:09,304 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:49:10,116 INFO  [root] No of ion clusters:10 (Memory usage:405MB)
2021-11-17 15:49:10,116 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_815_818_PeakCluster.serFS...
2021-11-17 15:49:10,117 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:49:10,931 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:49:11,383 INFO  [root] ==================================================================================
2021-11-17 15:49:11,383 INFO  [root] Processing DIA MS2 (mz range):812.0_815.0( 56/61 )
2021-11-17 15:49:11,506 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:49:11,506 INFO  [root] Smoothing detected signals......
2021-11-17 15:49:13,838 INFO  [root] 240863 Peak curves found (Memory usage:376MB)
2021-11-17 15:49:13,840 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:49:13,840 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:49:14,649 INFO  [root] No of ion clusters:15 (Memory usage:394MB)
2021-11-17 15:49:14,649 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_812_815_PeakCluster.serFS...
2021-11-17 15:49:14,650 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:49:15,514 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:49:15,934 INFO  [root] ==================================================================================
2021-11-17 15:49:15,934 INFO  [root] Processing DIA MS2 (mz range):809.0_812.0( 57/61 )
2021-11-17 15:49:16,010 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:49:16,010 INFO  [root] Smoothing detected signals......
2021-11-17 15:49:17,344 INFO  [root] 233095 Peak curves found (Memory usage:371MB)
2021-11-17 15:49:17,346 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:49:17,346 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:49:18,043 INFO  [root] No of ion clusters:20 (Memory usage:388MB)
2021-11-17 15:49:18,043 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_809_812_PeakCluster.serFS...
2021-11-17 15:49:18,044 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:49:18,787 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:49:19,218 INFO  [root] ==================================================================================
2021-11-17 15:49:19,218 INFO  [root] Processing DIA MS2 (mz range):806.0_809.0( 58/61 )
2021-11-17 15:49:19,298 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:49:19,298 INFO  [root] Smoothing detected signals......
2021-11-17 15:49:20,726 INFO  [root] 246859 Peak curves found (Memory usage:377MB)
2021-11-17 15:49:20,727 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:49:20,727 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:49:21,491 INFO  [root] No of ion clusters:17 (Memory usage:396MB)
2021-11-17 15:49:21,491 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_806_809_PeakCluster.serFS...
2021-11-17 15:49:21,492 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:49:22,518 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:49:22,994 INFO  [root] ==================================================================================
2021-11-17 15:49:22,994 INFO  [root] Processing DIA MS2 (mz range):803.0_806.0( 59/61 )
2021-11-17 15:49:23,079 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:49:23,079 INFO  [root] Smoothing detected signals......
2021-11-17 15:49:25,181 INFO  [root] 248597 Peak curves found (Memory usage:381MB)
2021-11-17 15:49:25,184 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:49:25,184 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:49:25,980 INFO  [root] No of ion clusters:9 (Memory usage:400MB)
2021-11-17 15:49:25,980 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_803_806_PeakCluster.serFS...
2021-11-17 15:49:25,981 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:49:26,795 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:49:27,210 INFO  [root] ==================================================================================
2021-11-17 15:49:27,211 INFO  [root] Processing DIA MS2 (mz range):800.0_803.0( 60/61 )
2021-11-17 15:49:27,268 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:49:27,268 INFO  [root] Smoothing detected signals......
2021-11-17 15:49:28,211 INFO  [root] 149913 Peak curves found (Memory usage:340MB)
2021-11-17 15:49:28,213 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:49:28,213 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:49:28,787 INFO  [root] No of ion clusters:18 (Memory usage:351MB)
2021-11-17 15:49:28,787 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_800_803_PeakCluster.serFS...
2021-11-17 15:49:28,787 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:49:29,417 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:49:29,841 INFO  [root] ==================================================================================
2021-11-17 15:49:29,841 INFO  [root] Processing DIA MS2 (mz range):797.0_800.0( 61/61 )
2021-11-17 15:49:29,883 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:49:29,883 INFO  [root] Smoothing detected signals......
2021-11-17 15:49:32,587 INFO  [root] 119936 Peak curves found (Memory usage:338MB)
2021-11-17 15:49:32,589 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:49:32,589 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:49:33,094 INFO  [root] No of ion clusters:107 (Memory usage:347MB)
2021-11-17 15:49:33,094 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_797_800_PeakCluster.serFS...
2021-11-17 15:49:33,095 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:49:34,640 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:49:35,468 INFO  [root] ==================================================================================
2021-11-17 15:49:37,700 INFO  [root] C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.mzXML processed time:0 hour, 3 min, 50 sec
2021-11-17 15:49:37,700 INFO  [root] Job complete
2021-11-17 15:49:37,701 INFO  [root] =================================================================================================
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
=================================================================================================
DIA-Umpire singal extraction analysis  (version: v2.2.3)
(c) University of Michigan
2021-11-17 15:49:45,119 INFO  [root] Version: v2.2.3
2021-11-17 15:49:45,119 INFO  [root] Parameter file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
2021-11-17 15:49:45,120 INFO  [root] Spectra file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.mzXML
2021-11-17 15:49:45,122 INFO  [root] 
2021-11-17 15:49:45,122 INFO  [root] ####################################################################################################
2021-11-17 15:49:45,122 INFO  [root] #No of threads
2021-11-17 15:49:45,122 INFO  [root] Thread = 7
2021-11-17 15:49:45,122 INFO  [root] ####################################################################################################
2021-11-17 15:49:45,122 INFO  [root] 
2021-11-17 15:49:45,122 INFO  [root] ## omit Thread
2021-11-17 15:49:45,122 INFO  [root] 
2021-11-17 15:49:45,122 INFO  [root] #Precursor-fragments grouping parameters
2021-11-17 15:49:45,122 INFO  [root] RPmax = 25
2021-11-17 15:49:45,122 INFO  [root] RFmax = 500
2021-11-17 15:49:45,123 INFO  [root] CorrThreshold = 0
2021-11-17 15:49:45,123 INFO  [root] DeltaApex = 0.2
2021-11-17 15:49:45,123 INFO  [root] RTOverlap = 0.3
2021-11-17 15:49:45,123 INFO  [root] 
2021-11-17 15:49:45,123 INFO  [root] #Fragment intensity adjustments
2021-11-17 15:49:45,124 INFO  [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2021-11-17 15:49:45,124 INFO  [root] AdjustFragIntensity = true
2021-11-17 15:49:45,124 INFO  [root] BoostComplementaryIon = false
2021-11-17 15:49:45,124 INFO  [root] 
2021-11-17 15:49:45,124 INFO  [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2021-11-17 15:49:45,124 INFO  [root] ExportPrecursorPeak = false
2021-11-17 15:49:45,124 INFO  [root] 
2021-11-17 15:49:45,124 INFO  [root] Q1 = true
2021-11-17 15:49:45,124 INFO  [root] Q2 = true
2021-11-17 15:49:45,124 INFO  [root] Q3 = true
2021-11-17 15:49:45,124 INFO  [root] 
2021-11-17 15:49:45,124 INFO  [root] #Signal extraction: mass accuracy and resolution
2021-11-17 15:49:45,124 INFO  [root] # resolution parameter matters only for data generated in profile mode
2021-11-17 15:49:45,124 INFO  [root] SE.MS1PPM = 10
2021-11-17 15:49:45,124 INFO  [root] SE.MS2PPM = 10
2021-11-17 15:49:45,124 INFO  [root] SE.Resolution = 60000
2021-11-17 15:49:45,124 INFO  [root] 
2021-11-17 15:49:45,124 INFO  [root] #Signal extraction: signal to noise filter
2021-11-17 15:49:45,124 INFO  [root] SE.SN = 1.1
2021-11-17 15:49:45,125 INFO  [root] SE.MS2SN = 1.1
2021-11-17 15:49:45,125 INFO  [root] 
2021-11-17 15:49:45,125 INFO  [root] #Signal extraction: minimum signal intensity filter
2021-11-17 15:49:45,125 INFO  [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2021-11-17 15:49:45,125 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2021-11-17 15:49:45,125 INFO  [root] SE.EstimateBG = false
2021-11-17 15:49:45,125 INFO  [root] SE.MinMSIntensity = 1
2021-11-17 15:49:45,125 INFO  [root] SE.MinMSMSIntensity = 1
2021-11-17 15:49:45,125 INFO  [root] 
2021-11-17 15:49:45,125 INFO  [root] #Signal extraction: peak curve detection and isotope grouping
2021-11-17 15:49:45,125 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2021-11-17 15:49:45,125 INFO  [root] SE.NoMissedScan = 1
2021-11-17 15:49:45,125 INFO  [root] SE.MaxCurveRTRange = 2
2021-11-17 15:49:45,125 INFO  [root] SE.RemoveGroupedPeaks = true
2021-11-17 15:49:45,125 INFO  [root] SE.RemoveGroupedPeaksRTOverlap = 0.3
2021-11-17 15:49:45,148 INFO  [root] SE.RemoveGroupedPeaksCorr = 0.3
2021-11-17 15:49:45,148 INFO  [root] SE.MinNoPeakCluster = 2
2021-11-17 15:49:45,148 INFO  [root] SE.MaxNoPeakCluster = 4
2021-11-17 15:49:45,148 INFO  [root] 
2021-11-17 15:49:45,148 INFO  [root] #Signal extraction: filtering of MS1 features
2021-11-17 15:49:45,149 INFO  [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2021-11-17 15:49:45,149 INFO  [root] SE.IsoPattern = 0.3
2021-11-17 15:49:45,149 INFO  [root] SE.MassDefectFilter = false
2021-11-17 15:49:45,149 INFO  [root] SE.MassDefectOffset = 0.1
2021-11-17 15:49:45,149 INFO  [root] 
2021-11-17 15:49:45,149 INFO  [root] #Signal extraction: other
2021-11-17 15:49:45,149 INFO  [root] SE.StartCharge = 1
2021-11-17 15:49:45,150 INFO  [root] SE.EndCharge = 5
2021-11-17 15:49:45,150 INFO  [root] SE.MS2StartCharge = 2
2021-11-17 15:49:45,150 INFO  [root] SE.MS2EndCharge = 5
2021-11-17 15:49:45,150 INFO  [root] SE.MinFrag = 10
2021-11-17 15:49:45,150 INFO  [root] SE.StartRT = 0
2021-11-17 15:49:45,150 INFO  [root] SE.EndRT = 9999
2021-11-17 15:49:45,150 INFO  [root] SE.MinMZ = 200
2021-11-17 15:49:45,150 INFO  [root] SE.MinPrecursorMass = 600
2021-11-17 15:49:45,150 INFO  [root] SE.MaxPrecursorMass = 5000
2021-11-17 15:49:45,151 INFO  [root] 
2021-11-17 15:49:45,151 INFO  [root] 
2021-11-17 15:49:45,151 INFO  [root] #Isolation window setting
2021-11-17 15:49:45,151 INFO  [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2021-11-17 15:49:45,151 INFO  [root] WindowType = SWATH
2021-11-17 15:49:45,151 INFO  [root] 
2021-11-17 15:49:45,151 INFO  [root] #Fix window size (For SWATH)
2021-11-17 15:49:45,151 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:49:45,151 INFO  [root] WindowSize = 10
2021-11-17 15:49:45,151 INFO  [root] 
2021-11-17 15:49:45,151 INFO  [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2021-11-17 15:49:45,151 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:49:45,151 INFO  [root] ==window setting begin
2021-11-17 15:49:45,151 INFO  [root] 
2021-11-17 15:49:45,152 INFO  [root] =================================================================================================
2021-11-17 15:49:45,152 INFO  [root] Processing C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.mzXML....
2021-11-17 15:49:45,160 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_diasetting.ser...
2021-11-17 15:49:45,173 INFO  [root] Writing parameter to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_params.ser...
2021-11-17 15:49:45,176 INFO  [root] Module A: Signal extraction
2021-11-17 15:49:51,491 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_diasetting.ser...
2021-11-17 15:49:51,964 INFO  [root] Processing MS1 peak detection
2021-11-17 15:49:51,965 INFO  [root] MS1 average cycle time : 2.6700304 seconds
2021-11-17 15:49:58,721 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:49:58,721 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:03,012 INFO  [root] 368206 Peak curves found (Memory usage:421MB)
2021-11-17 15:50:03,012 INFO  [root] Inclusion mz values found: 0/0
2021-11-17 15:50:03,012 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:03,012 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:13,867 INFO  [root] No of ion clusters:35509 (Memory usage:224MB)
2021-11-17 15:50:13,898 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_PeakCluster.serFS...
2021-11-17 15:50:14,228 INFO  [root] ==================================================================================
2021-11-17 15:50:14,229 INFO  [root] Processing DIA MS2 (mz range):977.0_980.0( 1/61 )
2021-11-17 15:50:14,341 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:14,341 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:16,049 INFO  [root] 107030 Peak curves found (Memory usage:292MB)
2021-11-17 15:50:16,056 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:16,056 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:16,554 INFO  [root] No of ion clusters:47 (Memory usage:300MB)
2021-11-17 15:50:16,554 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_977_980_PeakCluster.serFS...
2021-11-17 15:50:16,555 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:17,808 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:18,681 INFO  [root] ==================================================================================
2021-11-17 15:50:18,681 INFO  [root] Processing DIA MS2 (mz range):974.0_977.0( 2/61 )
2021-11-17 15:50:18,802 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:18,802 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:20,182 INFO  [root] 130126 Peak curves found (Memory usage:286MB)
2021-11-17 15:50:20,185 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:20,185 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:20,669 INFO  [root] No of ion clusters:29 (Memory usage:296MB)
2021-11-17 15:50:20,669 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_974_977_PeakCluster.serFS...
2021-11-17 15:50:20,670 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:21,277 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:21,732 INFO  [root] ==================================================================================
2021-11-17 15:50:21,733 INFO  [root] Processing DIA MS2 (mz range):971.0_974.0( 3/61 )
2021-11-17 15:50:21,830 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:21,830 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:23,736 INFO  [root] 198078 Peak curves found (Memory usage:315MB)
2021-11-17 15:50:23,738 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:23,739 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:24,359 INFO  [root] No of ion clusters:16 (Memory usage:330MB)
2021-11-17 15:50:24,359 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_971_974_PeakCluster.serFS...
2021-11-17 15:50:24,360 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:24,980 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:25,378 INFO  [root] ==================================================================================
2021-11-17 15:50:25,378 INFO  [root] Processing DIA MS2 (mz range):968.0_971.0( 4/61 )
2021-11-17 15:50:25,436 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:25,436 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:26,410 INFO  [root] 194510 Peak curves found (Memory usage:312MB)
2021-11-17 15:50:26,411 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:26,411 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:27,003 INFO  [root] No of ion clusters:22 (Memory usage:327MB)
2021-11-17 15:50:27,003 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_968_971_PeakCluster.serFS...
2021-11-17 15:50:27,004 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:27,562 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:27,947 INFO  [root] ==================================================================================
2021-11-17 15:50:27,947 INFO  [root] Processing DIA MS2 (mz range):965.0_968.0( 5/61 )
2021-11-17 15:50:28,014 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:28,014 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:29,092 INFO  [root] 210200 Peak curves found (Memory usage:320MB)
2021-11-17 15:50:29,094 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:29,094 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:29,751 INFO  [root] No of ion clusters:10 (Memory usage:336MB)
2021-11-17 15:50:29,751 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_965_968_PeakCluster.serFS...
2021-11-17 15:50:29,752 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:30,323 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:30,664 INFO  [root] ==================================================================================
2021-11-17 15:50:30,664 INFO  [root] Processing DIA MS2 (mz range):962.0_965.0( 6/61 )
2021-11-17 15:50:30,742 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:30,742 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:32,526 INFO  [root] 242330 Peak curves found (Memory usage:336MB)
2021-11-17 15:50:32,530 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:32,530 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:33,261 INFO  [root] No of ion clusters:26 (Memory usage:356MB)
2021-11-17 15:50:33,261 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_962_965_PeakCluster.serFS...
2021-11-17 15:50:33,262 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:34,019 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:34,412 INFO  [root] ==================================================================================
2021-11-17 15:50:34,412 INFO  [root] Processing DIA MS2 (mz range):959.0_962.0( 7/61 )
2021-11-17 15:50:34,491 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:34,491 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:37,208 INFO  [root] 247332 Peak curves found (Memory usage:341MB)
2021-11-17 15:50:37,210 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:37,210 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:38,062 INFO  [root] No of ion clusters:16 (Memory usage:361MB)
2021-11-17 15:50:38,062 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_959_962_PeakCluster.serFS...
2021-11-17 15:50:38,062 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:38,696 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:39,040 INFO  [root] ==================================================================================
2021-11-17 15:50:39,041 INFO  [root] Processing DIA MS2 (mz range):956.0_959.0( 8/61 )
2021-11-17 15:50:39,116 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:39,116 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:40,626 INFO  [root] 264767 Peak curves found (Memory usage:348MB)
2021-11-17 15:50:40,627 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:40,628 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:41,561 INFO  [root] No of ion clusters:24 (Memory usage:368MB)
2021-11-17 15:50:41,561 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_956_959_PeakCluster.serFS...
2021-11-17 15:50:41,562 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:42,247 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:42,636 INFO  [root] ==================================================================================
2021-11-17 15:50:42,636 INFO  [root] Processing DIA MS2 (mz range):953.0_956.0( 9/61 )
2021-11-17 15:50:42,746 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:42,746 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:46,289 INFO  [root] 244300 Peak curves found (Memory usage:346MB)
2021-11-17 15:50:46,291 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:46,291 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:47,127 INFO  [root] No of ion clusters:29 (Memory usage:365MB)
2021-11-17 15:50:47,127 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_953_956_PeakCluster.serFS...
2021-11-17 15:50:47,128 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:47,802 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:48,235 INFO  [root] ==================================================================================
2021-11-17 15:50:48,235 INFO  [root] Processing DIA MS2 (mz range):950.0_953.0( 10/61 )
2021-11-17 15:50:48,330 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:48,330 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:50,276 INFO  [root] 265016 Peak curves found (Memory usage:354MB)
2021-11-17 15:50:50,278 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:50,278 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:51,107 INFO  [root] No of ion clusters:18 (Memory usage:374MB)
2021-11-17 15:50:51,107 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_950_953_PeakCluster.serFS...
2021-11-17 15:50:51,108 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:51,766 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:52,167 INFO  [root] ==================================================================================
2021-11-17 15:50:52,167 INFO  [root] Processing DIA MS2 (mz range):947.0_950.0( 11/61 )
2021-11-17 15:50:52,261 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:52,261 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:54,040 INFO  [root] 262471 Peak curves found (Memory usage:355MB)
2021-11-17 15:50:54,041 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:54,042 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:54,904 INFO  [root] No of ion clusters:30 (Memory usage:375MB)
2021-11-17 15:50:54,905 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_947_950_PeakCluster.serFS...
2021-11-17 15:50:54,906 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:55,624 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:56,013 INFO  [root] ==================================================================================
2021-11-17 15:50:56,013 INFO  [root] Processing DIA MS2 (mz range):944.0_947.0( 12/61 )
2021-11-17 15:50:56,104 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:56,104 INFO  [root] Smoothing detected signals......
2021-11-17 15:50:57,952 INFO  [root] 264208 Peak curves found (Memory usage:358MB)
2021-11-17 15:50:57,954 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:50:57,954 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:50:58,718 INFO  [root] No of ion clusters:31 (Memory usage:378MB)
2021-11-17 15:50:58,718 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_944_947_PeakCluster.serFS...
2021-11-17 15:50:58,719 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:50:59,399 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:50:59,701 INFO  [root] ==================================================================================
2021-11-17 15:50:59,702 INFO  [root] Processing DIA MS2 (mz range):941.0_944.0( 13/61 )
2021-11-17 15:50:59,778 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:50:59,778 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:01,526 INFO  [root] 248816 Peak curves found (Memory usage:351MB)
2021-11-17 15:51:01,528 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:01,528 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:02,289 INFO  [root] No of ion clusters:21 (Memory usage:370MB)
2021-11-17 15:51:02,290 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_941_944_PeakCluster.serFS...
2021-11-17 15:51:02,290 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:02,858 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:03,225 INFO  [root] ==================================================================================
2021-11-17 15:51:03,225 INFO  [root] Processing DIA MS2 (mz range):938.0_941.0( 14/61 )
2021-11-17 15:51:03,310 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:03,310 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:05,649 INFO  [root] 268157 Peak curves found (Memory usage:361MB)
2021-11-17 15:51:05,651 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:05,651 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:06,422 INFO  [root] No of ion clusters:32 (Memory usage:381MB)
2021-11-17 15:51:06,422 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_938_941_PeakCluster.serFS...
2021-11-17 15:51:06,423 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:07,045 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:07,426 INFO  [root] ==================================================================================
2021-11-17 15:51:07,426 INFO  [root] Processing DIA MS2 (mz range):935.0_938.0( 15/61 )
2021-11-17 15:51:07,511 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:07,511 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:09,987 INFO  [root] 270538 Peak curves found (Memory usage:363MB)
2021-11-17 15:51:09,990 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:09,991 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:10,788 INFO  [root] No of ion clusters:51 (Memory usage:384MB)
2021-11-17 15:51:10,788 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_935_938_PeakCluster.serFS...
2021-11-17 15:51:10,789 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:11,639 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:12,096 INFO  [root] ==================================================================================
2021-11-17 15:51:12,096 INFO  [root] Processing DIA MS2 (mz range):932.0_935.0( 16/61 )
2021-11-17 15:51:12,182 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:12,182 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:13,752 INFO  [root] 235908 Peak curves found (Memory usage:347MB)
2021-11-17 15:51:13,754 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:13,754 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:14,477 INFO  [root] No of ion clusters:20 (Memory usage:365MB)
2021-11-17 15:51:14,477 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_932_935_PeakCluster.serFS...
2021-11-17 15:51:14,478 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:15,265 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:15,692 INFO  [root] ==================================================================================
2021-11-17 15:51:15,692 INFO  [root] Processing DIA MS2 (mz range):929.0_932.0( 17/61 )
2021-11-17 15:51:15,782 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:15,782 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:17,088 INFO  [root] 222130 Peak curves found (Memory usage:342MB)
2021-11-17 15:51:17,090 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:17,090 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:17,841 INFO  [root] No of ion clusters:21 (Memory usage:359MB)
2021-11-17 15:51:17,841 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_929_932_PeakCluster.serFS...
2021-11-17 15:51:17,842 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:18,447 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:18,845 INFO  [root] ==================================================================================
2021-11-17 15:51:18,845 INFO  [root] Processing DIA MS2 (mz range):926.0_929.0( 18/61 )
2021-11-17 15:51:18,916 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:18,916 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:20,125 INFO  [root] 208274 Peak curves found (Memory usage:339MB)
2021-11-17 15:51:20,127 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:20,127 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:20,815 INFO  [root] No of ion clusters:20 (Memory usage:355MB)
2021-11-17 15:51:20,815 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_926_929_PeakCluster.serFS...
2021-11-17 15:51:20,816 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:21,479 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:21,885 INFO  [root] ==================================================================================
2021-11-17 15:51:21,885 INFO  [root] Processing DIA MS2 (mz range):923.0_926.0( 19/61 )
2021-11-17 15:51:21,948 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:21,948 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:23,040 INFO  [root] 208849 Peak curves found (Memory usage:339MB)
2021-11-17 15:51:23,042 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:23,042 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:23,708 INFO  [root] No of ion clusters:14 (Memory usage:355MB)
2021-11-17 15:51:23,708 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_923_926_PeakCluster.serFS...
2021-11-17 15:51:23,709 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:24,427 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:24,800 INFO  [root] ==================================================================================
2021-11-17 15:51:24,800 INFO  [root] Processing DIA MS2 (mz range):920.0_923.0( 20/61 )
2021-11-17 15:51:24,871 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:24,871 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:26,006 INFO  [root] 226060 Peak curves found (Memory usage:346MB)
2021-11-17 15:51:26,008 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:26,008 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:26,687 INFO  [root] No of ion clusters:20 (Memory usage:363MB)
2021-11-17 15:51:26,687 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_920_923_PeakCluster.serFS...
2021-11-17 15:51:26,687 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:27,287 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:27,657 INFO  [root] ==================================================================================
2021-11-17 15:51:27,658 INFO  [root] Processing DIA MS2 (mz range):917.0_920.0( 21/61 )
2021-11-17 15:51:27,727 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:27,727 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:29,625 INFO  [root] 209031 Peak curves found (Memory usage:340MB)
2021-11-17 15:51:29,628 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:29,628 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:30,264 INFO  [root] No of ion clusters:17 (Memory usage:356MB)
2021-11-17 15:51:30,264 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_917_920_PeakCluster.serFS...
2021-11-17 15:51:30,265 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:30,777 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:31,123 INFO  [root] ==================================================================================
2021-11-17 15:51:31,123 INFO  [root] Processing DIA MS2 (mz range):914.0_917.0( 22/61 )
2021-11-17 15:51:31,185 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:31,185 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:32,197 INFO  [root] 212235 Peak curves found (Memory usage:341MB)
2021-11-17 15:51:32,199 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:32,199 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:32,860 INFO  [root] No of ion clusters:24 (Memory usage:357MB)
2021-11-17 15:51:32,860 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_914_917_PeakCluster.serFS...
2021-11-17 15:51:32,861 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:33,294 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:33,678 INFO  [root] ==================================================================================
2021-11-17 15:51:33,678 INFO  [root] Processing DIA MS2 (mz range):911.0_914.0( 23/61 )
2021-11-17 15:51:33,741 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:33,741 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:34,899 INFO  [root] 203885 Peak curves found (Memory usage:339MB)
2021-11-17 15:51:34,901 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:34,901 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:35,531 INFO  [root] No of ion clusters:25 (Memory usage:355MB)
2021-11-17 15:51:35,531 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_911_914_PeakCluster.serFS...
2021-11-17 15:51:35,532 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:36,112 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:36,485 INFO  [root] ==================================================================================
2021-11-17 15:51:36,485 INFO  [root] Processing DIA MS2 (mz range):908.0_911.0( 24/61 )
2021-11-17 15:51:36,561 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:36,562 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:37,869 INFO  [root] 208247 Peak curves found (Memory usage:342MB)
2021-11-17 15:51:37,871 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:37,871 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:38,501 INFO  [root] No of ion clusters:20 (Memory usage:358MB)
2021-11-17 15:51:38,501 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_908_911_PeakCluster.serFS...
2021-11-17 15:51:38,502 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:39,094 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:39,456 INFO  [root] ==================================================================================
2021-11-17 15:51:39,457 INFO  [root] Processing DIA MS2 (mz range):905.0_908.0( 25/61 )
2021-11-17 15:51:39,535 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:39,535 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:40,626 INFO  [root] 211904 Peak curves found (Memory usage:344MB)
2021-11-17 15:51:40,628 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:40,628 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:41,312 INFO  [root] No of ion clusters:19 (Memory usage:360MB)
2021-11-17 15:51:41,312 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_905_908_PeakCluster.serFS...
2021-11-17 15:51:41,313 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:41,855 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:42,225 INFO  [root] ==================================================================================
2021-11-17 15:51:42,225 INFO  [root] Processing DIA MS2 (mz range):902.0_905.0( 26/61 )
2021-11-17 15:51:42,297 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:42,298 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:43,490 INFO  [root] 244136 Peak curves found (Memory usage:358MB)
2021-11-17 15:51:43,491 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:43,491 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:44,263 INFO  [root] No of ion clusters:22 (Memory usage:376MB)
2021-11-17 15:51:44,263 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_902_905_PeakCluster.serFS...
2021-11-17 15:51:44,264 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:44,859 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:45,220 INFO  [root] ==================================================================================
2021-11-17 15:51:45,220 INFO  [root] Processing DIA MS2 (mz range):899.0_902.0( 27/61 )
2021-11-17 15:51:45,302 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:45,302 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:47,349 INFO  [root] 243764 Peak curves found (Memory usage:361MB)
2021-11-17 15:51:47,352 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:47,352 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:48,108 INFO  [root] No of ion clusters:21 (Memory usage:380MB)
2021-11-17 15:51:48,108 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_899_902_PeakCluster.serFS...
2021-11-17 15:51:48,109 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:48,975 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:49,374 INFO  [root] ==================================================================================
2021-11-17 15:51:49,374 INFO  [root] Processing DIA MS2 (mz range):896.0_899.0( 28/61 )
2021-11-17 15:51:49,457 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:49,457 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:50,959 INFO  [root] 263293 Peak curves found (Memory usage:366MB)
2021-11-17 15:51:50,963 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:50,963 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:51,847 INFO  [root] No of ion clusters:31 (Memory usage:387MB)
2021-11-17 15:51:51,847 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_896_899_PeakCluster.serFS...
2021-11-17 15:51:51,848 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:52,683 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:53,140 INFO  [root] ==================================================================================
2021-11-17 15:51:53,141 INFO  [root] Processing DIA MS2 (mz range):893.0_896.0( 29/61 )
2021-11-17 15:51:53,228 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:53,228 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:54,640 INFO  [root] 246579 Peak curves found (Memory usage:361MB)
2021-11-17 15:51:54,642 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:54,642 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:55,393 INFO  [root] No of ion clusters:28 (Memory usage:380MB)
2021-11-17 15:51:55,393 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_893_896_PeakCluster.serFS...
2021-11-17 15:51:55,394 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:56,418 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:51:56,855 INFO  [root] ==================================================================================
2021-11-17 15:51:56,855 INFO  [root] Processing DIA MS2 (mz range):890.0_893.0( 30/61 )
2021-11-17 15:51:56,945 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:51:56,945 INFO  [root] Smoothing detected signals......
2021-11-17 15:51:58,342 INFO  [root] 254495 Peak curves found (Memory usage:363MB)
2021-11-17 15:51:58,343 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:51:58,343 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:51:59,095 INFO  [root] No of ion clusters:12 (Memory usage:382MB)
2021-11-17 15:51:59,095 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_890_893_PeakCluster.serFS...
2021-11-17 15:51:59,096 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:51:59,908 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:00,361 INFO  [root] ==================================================================================
2021-11-17 15:52:00,361 INFO  [root] Processing DIA MS2 (mz range):887.0_890.0( 31/61 )
2021-11-17 15:52:00,450 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:00,450 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:01,951 INFO  [root] 253576 Peak curves found (Memory usage:366MB)
2021-11-17 15:52:01,953 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:01,953 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:02,670 INFO  [root] No of ion clusters:24 (Memory usage:385MB)
2021-11-17 15:52:02,670 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_887_890_PeakCluster.serFS...
2021-11-17 15:52:02,670 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:03,569 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:03,983 INFO  [root] ==================================================================================
2021-11-17 15:52:03,983 INFO  [root] Processing DIA MS2 (mz range):884.0_887.0( 32/61 )
2021-11-17 15:52:04,071 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:04,071 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:05,535 INFO  [root] 271939 Peak curves found (Memory usage:373MB)
2021-11-17 15:52:05,536 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:05,537 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:06,337 INFO  [root] No of ion clusters:29 (Memory usage:393MB)
2021-11-17 15:52:06,337 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_884_887_PeakCluster.serFS...
2021-11-17 15:52:06,337 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:07,150 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:07,594 INFO  [root] ==================================================================================
2021-11-17 15:52:07,594 INFO  [root] Processing DIA MS2 (mz range):881.0_884.0( 33/61 )
2021-11-17 15:52:07,711 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:07,711 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:09,498 INFO  [root] 252805 Peak curves found (Memory usage:367MB)
2021-11-17 15:52:09,500 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:09,500 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:10,219 INFO  [root] No of ion clusters:20 (Memory usage:385MB)
2021-11-17 15:52:10,219 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_881_884_PeakCluster.serFS...
2021-11-17 15:52:10,220 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:10,996 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:11,367 INFO  [root] ==================================================================================
2021-11-17 15:52:11,368 INFO  [root] Processing DIA MS2 (mz range):878.0_881.0( 34/61 )
2021-11-17 15:52:11,444 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:11,444 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:12,748 INFO  [root] 244827 Peak curves found (Memory usage:363MB)
2021-11-17 15:52:12,750 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:12,750 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:13,504 INFO  [root] No of ion clusters:19 (Memory usage:381MB)
2021-11-17 15:52:13,504 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_878_881_PeakCluster.serFS...
2021-11-17 15:52:13,504 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:14,235 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:14,652 INFO  [root] ==================================================================================
2021-11-17 15:52:14,652 INFO  [root] Processing DIA MS2 (mz range):875.0_878.0( 35/61 )
2021-11-17 15:52:14,724 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:14,724 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:16,009 INFO  [root] 240456 Peak curves found (Memory usage:362MB)
2021-11-17 15:52:16,011 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:16,011 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:16,749 INFO  [root] No of ion clusters:15 (Memory usage:379MB)
2021-11-17 15:52:16,749 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_875_878_PeakCluster.serFS...
2021-11-17 15:52:16,750 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:17,465 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:17,898 INFO  [root] ==================================================================================
2021-11-17 15:52:17,898 INFO  [root] Processing DIA MS2 (mz range):872.0_875.0( 36/61 )
2021-11-17 15:52:17,988 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:17,988 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:19,727 INFO  [root] 241956 Peak curves found (Memory usage:364MB)
2021-11-17 15:52:19,730 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:19,731 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:20,528 INFO  [root] No of ion clusters:42 (Memory usage:382MB)
2021-11-17 15:52:20,529 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_872_875_PeakCluster.serFS...
2021-11-17 15:52:20,530 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:21,384 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:21,880 INFO  [root] ==================================================================================
2021-11-17 15:52:21,880 INFO  [root] Processing DIA MS2 (mz range):869.0_872.0( 37/61 )
2021-11-17 15:52:21,969 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:21,969 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:23,268 INFO  [root] 238609 Peak curves found (Memory usage:360MB)
2021-11-17 15:52:23,270 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:23,270 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:24,066 INFO  [root] No of ion clusters:13 (Memory usage:378MB)
2021-11-17 15:52:24,066 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_869_872_PeakCluster.serFS...
2021-11-17 15:52:24,067 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:24,633 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:24,988 INFO  [root] ==================================================================================
2021-11-17 15:52:24,988 INFO  [root] Processing DIA MS2 (mz range):866.0_869.0( 38/61 )
2021-11-17 15:52:25,057 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:25,057 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:26,205 INFO  [root] 214348 Peak curves found (Memory usage:351MB)
2021-11-17 15:52:26,207 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:26,207 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:26,905 INFO  [root] No of ion clusters:18 (Memory usage:367MB)
2021-11-17 15:52:26,905 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_866_869_PeakCluster.serFS...
2021-11-17 15:52:26,905 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:27,470 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:27,844 INFO  [root] ==================================================================================
2021-11-17 15:52:27,844 INFO  [root] Processing DIA MS2 (mz range):863.0_866.0( 39/61 )
2021-11-17 15:52:27,915 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:27,915 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:29,229 INFO  [root] 223187 Peak curves found (Memory usage:356MB)
2021-11-17 15:52:29,231 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:29,231 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:29,954 INFO  [root] No of ion clusters:20 (Memory usage:373MB)
2021-11-17 15:52:29,954 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_863_866_PeakCluster.serFS...
2021-11-17 15:52:29,954 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:30,651 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:31,028 INFO  [root] ==================================================================================
2021-11-17 15:52:31,028 INFO  [root] Processing DIA MS2 (mz range):860.0_863.0( 40/61 )
2021-11-17 15:52:31,120 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:31,120 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:32,737 INFO  [root] 265944 Peak curves found (Memory usage:374MB)
2021-11-17 15:52:32,738 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:32,738 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:33,518 INFO  [root] No of ion clusters:19 (Memory usage:394MB)
2021-11-17 15:52:33,518 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_860_863_PeakCluster.serFS...
2021-11-17 15:52:33,518 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:34,258 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:34,681 INFO  [root] ==================================================================================
2021-11-17 15:52:34,681 INFO  [root] Processing DIA MS2 (mz range):857.0_860.0( 41/61 )
2021-11-17 15:52:34,784 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:34,784 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:36,846 INFO  [root] 265715 Peak curves found (Memory usage:375MB)
2021-11-17 15:52:36,848 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:36,848 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:37,660 INFO  [root] No of ion clusters:13 (Memory usage:395MB)
2021-11-17 15:52:37,660 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_857_860_PeakCluster.serFS...
2021-11-17 15:52:37,661 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:38,538 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:38,955 INFO  [root] ==================================================================================
2021-11-17 15:52:38,955 INFO  [root] Processing DIA MS2 (mz range):854.0_857.0( 42/61 )
2021-11-17 15:52:39,035 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:39,035 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:40,455 INFO  [root] 250655 Peak curves found (Memory usage:368MB)
2021-11-17 15:52:40,456 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:40,456 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:41,215 INFO  [root] No of ion clusters:12 (Memory usage:387MB)
2021-11-17 15:52:41,216 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_854_857_PeakCluster.serFS...
2021-11-17 15:52:41,216 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:42,003 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:42,418 INFO  [root] ==================================================================================
2021-11-17 15:52:42,418 INFO  [root] Processing DIA MS2 (mz range):851.0_854.0( 43/61 )
2021-11-17 15:52:42,494 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:42,494 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:43,810 INFO  [root] 267287 Peak curves found (Memory usage:374MB)
2021-11-17 15:52:43,812 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:43,812 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:44,619 INFO  [root] No of ion clusters:21 (Memory usage:394MB)
2021-11-17 15:52:44,619 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_851_854_PeakCluster.serFS...
2021-11-17 15:52:44,620 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:45,221 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:45,607 INFO  [root] ==================================================================================
2021-11-17 15:52:45,607 INFO  [root] Processing DIA MS2 (mz range):848.0_851.0( 44/61 )
2021-11-17 15:52:45,697 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:45,697 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:47,687 INFO  [root] 268728 Peak curves found (Memory usage:378MB)
2021-11-17 15:52:47,689 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:47,689 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:48,452 INFO  [root] No of ion clusters:10 (Memory usage:399MB)
2021-11-17 15:52:48,452 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_848_851_PeakCluster.serFS...
2021-11-17 15:52:48,453 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:49,439 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:49,834 INFO  [root] ==================================================================================
2021-11-17 15:52:49,834 INFO  [root] Processing DIA MS2 (mz range):845.0_848.0( 45/61 )
2021-11-17 15:52:49,920 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:49,920 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:51,497 INFO  [root] 274687 Peak curves found (Memory usage:378MB)
2021-11-17 15:52:51,499 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:51,499 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:52,317 INFO  [root] No of ion clusters:16 (Memory usage:399MB)
2021-11-17 15:52:52,317 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_845_848_PeakCluster.serFS...
2021-11-17 15:52:52,318 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:53,284 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:53,742 INFO  [root] ==================================================================================
2021-11-17 15:52:53,742 INFO  [root] Processing DIA MS2 (mz range):842.0_845.0( 46/61 )
2021-11-17 15:52:53,814 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:53,814 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:55,033 INFO  [root] 247687 Peak curves found (Memory usage:366MB)
2021-11-17 15:52:55,034 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:55,034 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:55,785 INFO  [root] No of ion clusters:18 (Memory usage:385MB)
2021-11-17 15:52:55,785 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_842_845_PeakCluster.serFS...
2021-11-17 15:52:55,785 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:56,551 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:52:56,971 INFO  [root] ==================================================================================
2021-11-17 15:52:56,971 INFO  [root] Processing DIA MS2 (mz range):839.0_842.0( 47/61 )
2021-11-17 15:52:57,053 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:52:57,053 INFO  [root] Smoothing detected signals......
2021-11-17 15:52:58,385 INFO  [root] 262402 Peak curves found (Memory usage:373MB)
2021-11-17 15:52:58,387 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:52:58,387 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:52:59,179 INFO  [root] No of ion clusters:17 (Memory usage:393MB)
2021-11-17 15:52:59,179 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_839_842_PeakCluster.serFS...
2021-11-17 15:52:59,180 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:52:59,986 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:00,442 INFO  [root] ==================================================================================
2021-11-17 15:53:00,442 INFO  [root] Processing DIA MS2 (mz range):836.0_839.0( 48/61 )
2021-11-17 15:53:00,536 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:00,536 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:02,397 INFO  [root] 285087 Peak curves found (Memory usage:384MB)
2021-11-17 15:53:02,398 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:02,399 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:03,261 INFO  [root] No of ion clusters:16 (Memory usage:406MB)
2021-11-17 15:53:03,261 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_836_839_PeakCluster.serFS...
2021-11-17 15:53:03,262 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:04,291 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:04,722 INFO  [root] ==================================================================================
2021-11-17 15:53:04,722 INFO  [root] Processing DIA MS2 (mz range):833.0_836.0( 49/61 )
2021-11-17 15:53:04,809 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:04,809 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:06,551 INFO  [root] 299949 Peak curves found (Memory usage:390MB)
2021-11-17 15:53:06,553 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:06,553 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:07,427 INFO  [root] No of ion clusters:18 (Memory usage:412MB)
2021-11-17 15:53:07,427 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_833_836_PeakCluster.serFS...
2021-11-17 15:53:07,428 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:08,432 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:08,869 INFO  [root] ==================================================================================
2021-11-17 15:53:08,869 INFO  [root] Processing DIA MS2 (mz range):830.0_833.0( 50/61 )
2021-11-17 15:53:08,969 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:08,969 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:11,179 INFO  [root] 298476 Peak curves found (Memory usage:391MB)
2021-11-17 15:53:11,181 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:11,181 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:12,028 INFO  [root] No of ion clusters:14 (Memory usage:414MB)
2021-11-17 15:53:12,029 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_830_833_PeakCluster.serFS...
2021-11-17 15:53:12,029 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:13,143 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:13,538 INFO  [root] ==================================================================================
2021-11-17 15:53:13,538 INFO  [root] Processing DIA MS2 (mz range):827.0_830.0( 51/61 )
2021-11-17 15:53:13,639 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:13,639 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:15,819 INFO  [root] 324694 Peak curves found (Memory usage:401MB)
2021-11-17 15:53:15,820 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:15,820 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:16,756 INFO  [root] No of ion clusters:9 (Memory usage:425MB)
2021-11-17 15:53:16,756 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_827_830_PeakCluster.serFS...
2021-11-17 15:53:16,757 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:17,775 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:18,214 INFO  [root] ==================================================================================
2021-11-17 15:53:18,214 INFO  [root] Processing DIA MS2 (mz range):824.0_827.0( 52/61 )
2021-11-17 15:53:18,337 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:18,337 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:21,089 INFO  [root] 292776 Peak curves found (Memory usage:389MB)
2021-11-17 15:53:21,091 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:21,091 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:21,930 INFO  [root] No of ion clusters:20 (Memory usage:412MB)
2021-11-17 15:53:21,930 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_824_827_PeakCluster.serFS...
2021-11-17 15:53:21,931 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:23,056 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:23,497 INFO  [root] ==================================================================================
2021-11-17 15:53:23,497 INFO  [root] Processing DIA MS2 (mz range):821.0_824.0( 53/61 )
2021-11-17 15:53:23,592 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:23,592 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:25,908 INFO  [root] 315712 Peak curves found (Memory usage:396MB)
2021-11-17 15:53:25,910 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:25,910 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:26,848 INFO  [root] No of ion clusters:21 (Memory usage:420MB)
2021-11-17 15:53:26,849 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_821_824_PeakCluster.serFS...
2021-11-17 15:53:26,849 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:28,049 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:28,592 INFO  [root] ==================================================================================
2021-11-17 15:53:28,592 INFO  [root] Processing DIA MS2 (mz range):818.0_821.0( 54/61 )
2021-11-17 15:53:28,697 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:28,697 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:31,778 INFO  [root] 280286 Peak curves found (Memory usage:384MB)
2021-11-17 15:53:31,780 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:31,780 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:32,665 INFO  [root] No of ion clusters:15 (Memory usage:405MB)
2021-11-17 15:53:32,665 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_818_821_PeakCluster.serFS...
2021-11-17 15:53:32,666 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:33,848 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:34,336 INFO  [root] ==================================================================================
2021-11-17 15:53:34,336 INFO  [root] Processing DIA MS2 (mz range):815.0_818.0( 55/61 )
2021-11-17 15:53:34,426 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:34,426 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:36,027 INFO  [root] 267469 Peak curves found (Memory usage:377MB)
2021-11-17 15:53:36,029 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:36,029 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:36,875 INFO  [root] No of ion clusters:15 (Memory usage:397MB)
2021-11-17 15:53:36,875 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_815_818_PeakCluster.serFS...
2021-11-17 15:53:36,876 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:37,788 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:38,230 INFO  [root] ==================================================================================
2021-11-17 15:53:38,230 INFO  [root] Processing DIA MS2 (mz range):812.0_815.0( 56/61 )
2021-11-17 15:53:38,321 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:38,322 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:41,222 INFO  [root] 251462 Peak curves found (Memory usage:371MB)
2021-11-17 15:53:41,224 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:41,224 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:42,073 INFO  [root] No of ion clusters:25 (Memory usage:391MB)
2021-11-17 15:53:42,073 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_812_815_PeakCluster.serFS...
2021-11-17 15:53:42,074 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:43,010 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:43,445 INFO  [root] ==================================================================================
2021-11-17 15:53:43,445 INFO  [root] Processing DIA MS2 (mz range):809.0_812.0( 57/61 )
2021-11-17 15:53:43,521 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:43,521 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:44,860 INFO  [root] 255801 Peak curves found (Memory usage:371MB)
2021-11-17 15:53:44,862 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:44,862 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:45,648 INFO  [root] No of ion clusters:12 (Memory usage:390MB)
2021-11-17 15:53:45,648 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_809_812_PeakCluster.serFS...
2021-11-17 15:53:45,649 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:46,420 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:46,809 INFO  [root] ==================================================================================
2021-11-17 15:53:46,810 INFO  [root] Processing DIA MS2 (mz range):806.0_809.0( 58/61 )
2021-11-17 15:53:46,890 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:46,890 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:48,303 INFO  [root] 256222 Peak curves found (Memory usage:372MB)
2021-11-17 15:53:48,305 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:48,305 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:49,113 INFO  [root] No of ion clusters:23 (Memory usage:392MB)
2021-11-17 15:53:49,113 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_806_809_PeakCluster.serFS...
2021-11-17 15:53:49,114 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:49,994 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:50,432 INFO  [root] ==================================================================================
2021-11-17 15:53:50,432 INFO  [root] Processing DIA MS2 (mz range):803.0_806.0( 59/61 )
2021-11-17 15:53:50,542 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:50,542 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:52,911 INFO  [root] 276246 Peak curves found (Memory usage:383MB)
2021-11-17 15:53:52,913 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:52,913 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:53,748 INFO  [root] No of ion clusters:12 (Memory usage:404MB)
2021-11-17 15:53:53,748 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_803_806_PeakCluster.serFS...
2021-11-17 15:53:53,749 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:54,678 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:55,091 INFO  [root] ==================================================================================
2021-11-17 15:53:55,091 INFO  [root] Processing DIA MS2 (mz range):800.0_803.0( 60/61 )
2021-11-17 15:53:55,158 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:55,158 INFO  [root] Smoothing detected signals......
2021-11-17 15:53:56,626 INFO  [root] 172299 Peak curves found (Memory usage:342MB)
2021-11-17 15:53:56,628 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:53:56,628 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:53:57,208 INFO  [root] No of ion clusters:18 (Memory usage:355MB)
2021-11-17 15:53:57,208 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_800_803_PeakCluster.serFS...
2021-11-17 15:53:57,209 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:53:58,173 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:53:58,587 INFO  [root] ==================================================================================
2021-11-17 15:53:58,587 INFO  [root] Processing DIA MS2 (mz range):797.0_800.0( 61/61 )
2021-11-17 15:53:58,634 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:53:58,634 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:01,303 INFO  [root] 141090 Peak curves found (Memory usage:340MB)
2021-11-17 15:54:01,305 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:01,305 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:01,845 INFO  [root] No of ion clusters:113 (Memory usage:351MB)
2021-11-17 15:54:01,845 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_797_800_PeakCluster.serFS...
2021-11-17 15:54:01,846 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:03,921 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:04,862 INFO  [root] ==================================================================================
2021-11-17 15:54:07,029 INFO  [root] C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.mzXML processed time:0 hour, 4 min, 21 sec
2021-11-17 15:54:07,029 INFO  [root] Job complete
2021-11-17 15:54:07,029 INFO  [root] =================================================================================================
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
=================================================================================================
DIA-Umpire singal extraction analysis  (version: v2.2.3)
(c) University of Michigan
2021-11-17 15:54:14,473 INFO  [root] Version: v2.2.3
2021-11-17 15:54:14,474 INFO  [root] Parameter file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
2021-11-17 15:54:14,474 INFO  [root] Spectra file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.mzXML
2021-11-17 15:54:14,476 INFO  [root] 
2021-11-17 15:54:14,476 INFO  [root] ####################################################################################################
2021-11-17 15:54:14,476 INFO  [root] #No of threads
2021-11-17 15:54:14,476 INFO  [root] Thread = 7
2021-11-17 15:54:14,476 INFO  [root] ####################################################################################################
2021-11-17 15:54:14,476 INFO  [root] 
2021-11-17 15:54:14,476 INFO  [root] ## omit Thread
2021-11-17 15:54:14,476 INFO  [root] 
2021-11-17 15:54:14,476 INFO  [root] #Precursor-fragments grouping parameters
2021-11-17 15:54:14,476 INFO  [root] RPmax = 25
2021-11-17 15:54:14,476 INFO  [root] RFmax = 500
2021-11-17 15:54:14,476 INFO  [root] CorrThreshold = 0
2021-11-17 15:54:14,477 INFO  [root] DeltaApex = 0.2
2021-11-17 15:54:14,477 INFO  [root] RTOverlap = 0.3
2021-11-17 15:54:14,477 INFO  [root] 
2021-11-17 15:54:14,477 INFO  [root] #Fragment intensity adjustments
2021-11-17 15:54:14,477 INFO  [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2021-11-17 15:54:14,477 INFO  [root] AdjustFragIntensity = true
2021-11-17 15:54:14,477 INFO  [root] BoostComplementaryIon = false
2021-11-17 15:54:14,477 INFO  [root] 
2021-11-17 15:54:14,477 INFO  [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2021-11-17 15:54:14,477 INFO  [root] ExportPrecursorPeak = false
2021-11-17 15:54:14,477 INFO  [root] 
2021-11-17 15:54:14,477 INFO  [root] Q1 = true
2021-11-17 15:54:14,477 INFO  [root] Q2 = true
2021-11-17 15:54:14,477 INFO  [root] Q3 = true
2021-11-17 15:54:14,477 INFO  [root] 
2021-11-17 15:54:14,478 INFO  [root] #Signal extraction: mass accuracy and resolution
2021-11-17 15:54:14,478 INFO  [root] # resolution parameter matters only for data generated in profile mode
2021-11-17 15:54:14,478 INFO  [root] SE.MS1PPM = 10
2021-11-17 15:54:14,478 INFO  [root] SE.MS2PPM = 10
2021-11-17 15:54:14,478 INFO  [root] SE.Resolution = 60000
2021-11-17 15:54:14,478 INFO  [root] 
2021-11-17 15:54:14,478 INFO  [root] #Signal extraction: signal to noise filter
2021-11-17 15:54:14,478 INFO  [root] SE.SN = 1.1
2021-11-17 15:54:14,478 INFO  [root] SE.MS2SN = 1.1
2021-11-17 15:54:14,478 INFO  [root] 
2021-11-17 15:54:14,478 INFO  [root] #Signal extraction: minimum signal intensity filter
2021-11-17 15:54:14,478 INFO  [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2021-11-17 15:54:14,478 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2021-11-17 15:54:14,478 INFO  [root] SE.EstimateBG = false
2021-11-17 15:54:14,478 INFO  [root] SE.MinMSIntensity = 1
2021-11-17 15:54:14,478 INFO  [root] SE.MinMSMSIntensity = 1
2021-11-17 15:54:14,478 INFO  [root] 
2021-11-17 15:54:14,478 INFO  [root] #Signal extraction: peak curve detection and isotope grouping
2021-11-17 15:54:14,478 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2021-11-17 15:54:14,479 INFO  [root] SE.NoMissedScan = 1
2021-11-17 15:54:14,479 INFO  [root] SE.MaxCurveRTRange = 2
2021-11-17 15:54:14,479 INFO  [root] SE.RemoveGroupedPeaks = true
2021-11-17 15:54:14,479 INFO  [root] SE.RemoveGroupedPeaksRTOverlap = 0.3
2021-11-17 15:54:14,480 INFO  [root] SE.RemoveGroupedPeaksCorr = 0.3
2021-11-17 15:54:14,480 INFO  [root] SE.MinNoPeakCluster = 2
2021-11-17 15:54:14,480 INFO  [root] SE.MaxNoPeakCluster = 4
2021-11-17 15:54:14,480 INFO  [root] 
2021-11-17 15:54:14,480 INFO  [root] #Signal extraction: filtering of MS1 features
2021-11-17 15:54:14,480 INFO  [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2021-11-17 15:54:14,480 INFO  [root] SE.IsoPattern = 0.3
2021-11-17 15:54:14,481 INFO  [root] SE.MassDefectFilter = false
2021-11-17 15:54:14,481 INFO  [root] SE.MassDefectOffset = 0.1
2021-11-17 15:54:14,481 INFO  [root] 
2021-11-17 15:54:14,481 INFO  [root] #Signal extraction: other
2021-11-17 15:54:14,481 INFO  [root] SE.StartCharge = 1
2021-11-17 15:54:14,481 INFO  [root] SE.EndCharge = 5
2021-11-17 15:54:14,481 INFO  [root] SE.MS2StartCharge = 2
2021-11-17 15:54:14,481 INFO  [root] SE.MS2EndCharge = 5
2021-11-17 15:54:14,481 INFO  [root] SE.MinFrag = 10
2021-11-17 15:54:14,481 INFO  [root] SE.StartRT = 0
2021-11-17 15:54:14,481 INFO  [root] SE.EndRT = 9999
2021-11-17 15:54:14,481 INFO  [root] SE.MinMZ = 200
2021-11-17 15:54:14,481 INFO  [root] SE.MinPrecursorMass = 600
2021-11-17 15:54:14,482 INFO  [root] SE.MaxPrecursorMass = 5000
2021-11-17 15:54:14,482 INFO  [root] 
2021-11-17 15:54:14,482 INFO  [root] 
2021-11-17 15:54:14,482 INFO  [root] #Isolation window setting
2021-11-17 15:54:14,482 INFO  [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2021-11-17 15:54:14,482 INFO  [root] WindowType = SWATH
2021-11-17 15:54:14,482 INFO  [root] 
2021-11-17 15:54:14,482 INFO  [root] #Fix window size (For SWATH)
2021-11-17 15:54:14,482 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:54:14,482 INFO  [root] WindowSize = 10
2021-11-17 15:54:14,482 INFO  [root] 
2021-11-17 15:54:14,482 INFO  [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2021-11-17 15:54:14,482 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:54:14,482 INFO  [root] ==window setting begin
2021-11-17 15:54:14,482 INFO  [root] 
2021-11-17 15:54:14,482 INFO  [root] =================================================================================================
2021-11-17 15:54:14,482 INFO  [root] Processing C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.mzXML....
2021-11-17 15:54:14,486 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_diasetting.ser...
2021-11-17 15:54:14,495 INFO  [root] Writing parameter to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_params.ser...
2021-11-17 15:54:14,497 INFO  [root] Module A: Signal extraction
2021-11-17 15:54:16,967 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_diasetting.ser...
2021-11-17 15:54:17,472 INFO  [root] Processing MS1 peak detection
2021-11-17 15:54:17,474 INFO  [root] MS1 average cycle time : 2.6854253 seconds
2021-11-17 15:54:20,424 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:20,424 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:22,969 INFO  [root] 257026 Peak curves found (Memory usage:199MB)
2021-11-17 15:54:22,969 INFO  [root] Inclusion mz values found: 0/0
2021-11-17 15:54:22,969 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:22,970 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:28,613 INFO  [root] No of ion clusters:18894 (Memory usage:156MB)
2021-11-17 15:54:28,627 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_PeakCluster.serFS...
2021-11-17 15:54:28,838 INFO  [root] ==================================================================================
2021-11-17 15:54:28,839 INFO  [root] Processing DIA MS2 (mz range):977.0_980.0( 1/61 )
2021-11-17 15:54:28,910 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:28,910 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:29,491 INFO  [root] 30472 Peak curves found (Memory usage:182MB)
2021-11-17 15:54:29,496 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:29,496 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:29,752 INFO  [root] No of ion clusters:16 (Memory usage:184MB)
2021-11-17 15:54:29,752 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_977_980_PeakCluster.serFS...
2021-11-17 15:54:29,754 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:30,006 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:30,428 INFO  [root] ==================================================================================
2021-11-17 15:54:30,430 INFO  [root] Processing DIA MS2 (mz range):974.0_977.0( 2/61 )
2021-11-17 15:54:30,482 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:30,482 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:31,135 INFO  [root] 36097 Peak curves found (Memory usage:173MB)
2021-11-17 15:54:31,138 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:31,138 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:31,419 INFO  [root] No of ion clusters:4 (Memory usage:176MB)
2021-11-17 15:54:31,419 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_974_977_PeakCluster.serFS...
2021-11-17 15:54:31,420 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:31,546 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:31,800 INFO  [root] ==================================================================================
2021-11-17 15:54:31,803 INFO  [root] Processing DIA MS2 (mz range):971.0_974.0( 3/61 )
2021-11-17 15:54:31,862 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:31,862 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:32,350 INFO  [root] 67850 Peak curves found (Memory usage:185MB)
2021-11-17 15:54:32,353 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:32,353 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:32,635 INFO  [root] No of ion clusters:0 (Memory usage:190MB)
2021-11-17 15:54:32,635 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_971_974_PeakCluster.serFS...
2021-11-17 15:54:32,636 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:32,757 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:32,963 INFO  [root] ==================================================================================
2021-11-17 15:54:32,964 INFO  [root] Processing DIA MS2 (mz range):968.0_971.0( 4/61 )
2021-11-17 15:54:32,995 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:32,995 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:33,307 INFO  [root] 64536 Peak curves found (Memory usage:183MB)
2021-11-17 15:54:33,309 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:33,309 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:33,582 INFO  [root] No of ion clusters:3 (Memory usage:188MB)
2021-11-17 15:54:33,582 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_968_971_PeakCluster.serFS...
2021-11-17 15:54:33,583 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:33,738 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:33,950 INFO  [root] ==================================================================================
2021-11-17 15:54:33,950 INFO  [root] Processing DIA MS2 (mz range):965.0_968.0( 5/61 )
2021-11-17 15:54:33,979 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:33,980 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:34,288 INFO  [root] 69654 Peak curves found (Memory usage:186MB)
2021-11-17 15:54:34,290 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:34,291 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:34,611 INFO  [root] No of ion clusters:2 (Memory usage:192MB)
2021-11-17 15:54:34,611 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_965_968_PeakCluster.serFS...
2021-11-17 15:54:34,612 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:34,711 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:34,936 INFO  [root] ==================================================================================
2021-11-17 15:54:34,936 INFO  [root] Processing DIA MS2 (mz range):962.0_965.0( 6/61 )
2021-11-17 15:54:34,969 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:34,969 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:35,443 INFO  [root] 85095 Peak curves found (Memory usage:193MB)
2021-11-17 15:54:35,447 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:35,447 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:35,816 INFO  [root] No of ion clusters:8 (Memory usage:200MB)
2021-11-17 15:54:35,816 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_962_965_PeakCluster.serFS...
2021-11-17 15:54:35,817 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:35,976 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:36,224 INFO  [root] ==================================================================================
2021-11-17 15:54:36,224 INFO  [root] Processing DIA MS2 (mz range):959.0_962.0( 7/61 )
2021-11-17 15:54:36,263 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:36,263 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:36,757 INFO  [root] 78858 Peak curves found (Memory usage:191MB)
2021-11-17 15:54:36,759 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:36,759 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:37,066 INFO  [root] No of ion clusters:6 (Memory usage:198MB)
2021-11-17 15:54:37,067 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_959_962_PeakCluster.serFS...
2021-11-17 15:54:37,067 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:37,232 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:37,494 INFO  [root] ==================================================================================
2021-11-17 15:54:37,494 INFO  [root] Processing DIA MS2 (mz range):956.0_959.0( 8/61 )
2021-11-17 15:54:37,522 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:37,522 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:37,909 INFO  [root] 79408 Peak curves found (Memory usage:192MB)
2021-11-17 15:54:37,911 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:37,911 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:38,235 INFO  [root] No of ion clusters:1 (Memory usage:198MB)
2021-11-17 15:54:38,235 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_956_959_PeakCluster.serFS...
2021-11-17 15:54:38,236 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:38,343 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:38,547 INFO  [root] ==================================================================================
2021-11-17 15:54:38,547 INFO  [root] Processing DIA MS2 (mz range):953.0_956.0( 9/61 )
2021-11-17 15:54:38,580 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:38,580 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:39,109 INFO  [root] 69340 Peak curves found (Memory usage:189MB)
2021-11-17 15:54:39,111 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:39,111 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:39,387 INFO  [root] No of ion clusters:11 (Memory usage:194MB)
2021-11-17 15:54:39,387 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_953_956_PeakCluster.serFS...
2021-11-17 15:54:39,388 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:39,498 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:39,713 INFO  [root] ==================================================================================
2021-11-17 15:54:39,713 INFO  [root] Processing DIA MS2 (mz range):950.0_953.0( 10/61 )
2021-11-17 15:54:39,738 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:39,738 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:40,135 INFO  [root] 63745 Peak curves found (Memory usage:187MB)
2021-11-17 15:54:40,138 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:40,138 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:40,455 INFO  [root] No of ion clusters:5 (Memory usage:192MB)
2021-11-17 15:54:40,455 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_950_953_PeakCluster.serFS...
2021-11-17 15:54:40,456 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:40,548 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:40,772 INFO  [root] ==================================================================================
2021-11-17 15:54:40,772 INFO  [root] Processing DIA MS2 (mz range):947.0_950.0( 11/61 )
2021-11-17 15:54:40,798 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:40,798 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:41,105 INFO  [root] 58333 Peak curves found (Memory usage:185MB)
2021-11-17 15:54:41,107 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:41,107 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:41,371 INFO  [root] No of ion clusters:9 (Memory usage:190MB)
2021-11-17 15:54:41,371 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_947_950_PeakCluster.serFS...
2021-11-17 15:54:41,372 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:41,455 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:41,680 INFO  [root] ==================================================================================
2021-11-17 15:54:41,680 INFO  [root] Processing DIA MS2 (mz range):944.0_947.0( 12/61 )
2021-11-17 15:54:41,704 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:41,704 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:41,992 INFO  [root] 58379 Peak curves found (Memory usage:185MB)
2021-11-17 15:54:41,995 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:41,995 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:42,289 INFO  [root] No of ion clusters:9 (Memory usage:190MB)
2021-11-17 15:54:42,289 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_944_947_PeakCluster.serFS...
2021-11-17 15:54:42,290 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:42,349 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:42,552 INFO  [root] ==================================================================================
2021-11-17 15:54:42,552 INFO  [root] Processing DIA MS2 (mz range):941.0_944.0( 13/61 )
2021-11-17 15:54:42,577 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:42,577 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:42,953 INFO  [root] 59778 Peak curves found (Memory usage:187MB)
2021-11-17 15:54:42,955 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:42,955 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:43,236 INFO  [root] No of ion clusters:1 (Memory usage:191MB)
2021-11-17 15:54:43,237 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_941_944_PeakCluster.serFS...
2021-11-17 15:54:43,237 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:43,311 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:43,505 INFO  [root] ==================================================================================
2021-11-17 15:54:43,505 INFO  [root] Processing DIA MS2 (mz range):938.0_941.0( 14/61 )
2021-11-17 15:54:43,529 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:43,529 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:43,868 INFO  [root] 61111 Peak curves found (Memory usage:188MB)
2021-11-17 15:54:43,869 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:43,870 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:44,144 INFO  [root] No of ion clusters:9 (Memory usage:192MB)
2021-11-17 15:54:44,144 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_938_941_PeakCluster.serFS...
2021-11-17 15:54:44,145 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:44,207 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:44,405 INFO  [root] ==================================================================================
2021-11-17 15:54:44,405 INFO  [root] Processing DIA MS2 (mz range):935.0_938.0( 15/61 )
2021-11-17 15:54:44,430 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:44,430 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:44,728 INFO  [root] 57378 Peak curves found (Memory usage:187MB)
2021-11-17 15:54:44,731 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:44,731 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:45,008 INFO  [root] No of ion clusters:4 (Memory usage:191MB)
2021-11-17 15:54:45,008 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_935_938_PeakCluster.serFS...
2021-11-17 15:54:45,009 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:45,085 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:45,276 INFO  [root] ==================================================================================
2021-11-17 15:54:45,276 INFO  [root] Processing DIA MS2 (mz range):932.0_935.0( 16/61 )
2021-11-17 15:54:45,299 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:45,299 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:45,571 INFO  [root] 53685 Peak curves found (Memory usage:186MB)
2021-11-17 15:54:45,572 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:45,573 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:45,828 INFO  [root] No of ion clusters:10 (Memory usage:190MB)
2021-11-17 15:54:45,828 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_932_935_PeakCluster.serFS...
2021-11-17 15:54:45,829 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:45,892 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:46,094 INFO  [root] ==================================================================================
2021-11-17 15:54:46,094 INFO  [root] Processing DIA MS2 (mz range):929.0_932.0( 17/61 )
2021-11-17 15:54:46,117 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:46,117 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:46,390 INFO  [root] 52825 Peak curves found (Memory usage:186MB)
2021-11-17 15:54:46,392 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:46,392 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:46,636 INFO  [root] No of ion clusters:5 (Memory usage:190MB)
2021-11-17 15:54:46,636 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_929_932_PeakCluster.serFS...
2021-11-17 15:54:46,637 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:46,699 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:46,904 INFO  [root] ==================================================================================
2021-11-17 15:54:46,904 INFO  [root] Processing DIA MS2 (mz range):926.0_929.0( 18/61 )
2021-11-17 15:54:46,929 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:46,929 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:47,208 INFO  [root] 53230 Peak curves found (Memory usage:186MB)
2021-11-17 15:54:47,209 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:47,210 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:47,463 INFO  [root] No of ion clusters:6 (Memory usage:190MB)
2021-11-17 15:54:47,464 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_926_929_PeakCluster.serFS...
2021-11-17 15:54:47,464 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:47,525 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:47,730 INFO  [root] ==================================================================================
2021-11-17 15:54:47,731 INFO  [root] Processing DIA MS2 (mz range):923.0_926.0( 19/61 )
2021-11-17 15:54:47,755 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:47,755 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:48,020 INFO  [root] 51436 Peak curves found (Memory usage:186MB)
2021-11-17 15:54:48,021 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:48,021 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:48,271 INFO  [root] No of ion clusters:7 (Memory usage:190MB)
2021-11-17 15:54:48,271 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_923_926_PeakCluster.serFS...
2021-11-17 15:54:48,272 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:48,331 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:48,536 INFO  [root] ==================================================================================
2021-11-17 15:54:48,536 INFO  [root] Processing DIA MS2 (mz range):920.0_923.0( 20/61 )
2021-11-17 15:54:48,559 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:48,559 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:48,855 INFO  [root] 60529 Peak curves found (Memory usage:190MB)
2021-11-17 15:54:48,857 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:48,857 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:49,131 INFO  [root] No of ion clusters:3 (Memory usage:194MB)
2021-11-17 15:54:49,131 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_920_923_PeakCluster.serFS...
2021-11-17 15:54:49,132 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:49,201 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:49,411 INFO  [root] ==================================================================================
2021-11-17 15:54:49,411 INFO  [root] Processing DIA MS2 (mz range):917.0_920.0( 21/61 )
2021-11-17 15:54:49,439 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:49,439 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:49,821 INFO  [root] 60431 Peak curves found (Memory usage:191MB)
2021-11-17 15:54:49,822 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:49,822 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:50,088 INFO  [root] No of ion clusters:1 (Memory usage:196MB)
2021-11-17 15:54:50,088 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_917_920_PeakCluster.serFS...
2021-11-17 15:54:50,089 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:50,203 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:50,400 INFO  [root] ==================================================================================
2021-11-17 15:54:50,400 INFO  [root] Processing DIA MS2 (mz range):914.0_917.0( 22/61 )
2021-11-17 15:54:50,428 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:50,428 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:50,699 INFO  [root] 62623 Peak curves found (Memory usage:191MB)
2021-11-17 15:54:50,701 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:50,701 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:50,984 INFO  [root] No of ion clusters:8 (Memory usage:196MB)
2021-11-17 15:54:50,984 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_914_917_PeakCluster.serFS...
2021-11-17 15:54:50,984 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:51,054 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:51,254 INFO  [root] ==================================================================================
2021-11-17 15:54:51,254 INFO  [root] Processing DIA MS2 (mz range):911.0_914.0( 23/61 )
2021-11-17 15:54:51,277 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:51,277 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:51,542 INFO  [root] 60343 Peak curves found (Memory usage:191MB)
2021-11-17 15:54:51,543 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:51,544 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:51,819 INFO  [root] No of ion clusters:8 (Memory usage:195MB)
2021-11-17 15:54:51,819 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_911_914_PeakCluster.serFS...
2021-11-17 15:54:51,820 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:51,872 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:52,072 INFO  [root] ==================================================================================
2021-11-17 15:54:52,072 INFO  [root] Processing DIA MS2 (mz range):908.0_911.0( 24/61 )
2021-11-17 15:54:52,094 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:52,094 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:52,371 INFO  [root] 51509 Peak curves found (Memory usage:188MB)
2021-11-17 15:54:52,373 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:52,373 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:52,629 INFO  [root] No of ion clusters:6 (Memory usage:192MB)
2021-11-17 15:54:52,629 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_908_911_PeakCluster.serFS...
2021-11-17 15:54:52,630 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:52,694 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:52,910 INFO  [root] ==================================================================================
2021-11-17 15:54:52,910 INFO  [root] Processing DIA MS2 (mz range):905.0_908.0( 25/61 )
2021-11-17 15:54:52,930 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:52,930 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:53,168 INFO  [root] 51477 Peak curves found (Memory usage:188MB)
2021-11-17 15:54:53,169 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:53,170 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:53,423 INFO  [root] No of ion clusters:5 (Memory usage:192MB)
2021-11-17 15:54:53,423 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_905_908_PeakCluster.serFS...
2021-11-17 15:54:53,423 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:53,460 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:53,657 INFO  [root] ==================================================================================
2021-11-17 15:54:53,657 INFO  [root] Processing DIA MS2 (mz range):902.0_905.0( 26/61 )
2021-11-17 15:54:53,678 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:53,678 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:53,917 INFO  [root] 50213 Peak curves found (Memory usage:188MB)
2021-11-17 15:54:53,919 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:53,919 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:54,161 INFO  [root] No of ion clusters:5 (Memory usage:192MB)
2021-11-17 15:54:54,161 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_902_905_PeakCluster.serFS...
2021-11-17 15:54:54,162 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:54,198 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:54,393 INFO  [root] ==================================================================================
2021-11-17 15:54:54,393 INFO  [root] Processing DIA MS2 (mz range):899.0_902.0( 27/61 )
2021-11-17 15:54:54,414 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:54,414 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:54,698 INFO  [root] 52294 Peak curves found (Memory usage:190MB)
2021-11-17 15:54:54,700 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:54,700 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:54,959 INFO  [root] No of ion clusters:3 (Memory usage:194MB)
2021-11-17 15:54:54,959 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_899_902_PeakCluster.serFS...
2021-11-17 15:54:54,959 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:55,006 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:55,202 INFO  [root] ==================================================================================
2021-11-17 15:54:55,202 INFO  [root] Processing DIA MS2 (mz range):896.0_899.0( 28/61 )
2021-11-17 15:54:55,227 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:55,227 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:55,492 INFO  [root] 57069 Peak curves found (Memory usage:192MB)
2021-11-17 15:54:55,494 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:55,494 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:55,762 INFO  [root] No of ion clusters:9 (Memory usage:196MB)
2021-11-17 15:54:55,762 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_896_899_PeakCluster.serFS...
2021-11-17 15:54:55,763 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:55,873 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:56,094 INFO  [root] ==================================================================================
2021-11-17 15:54:56,094 INFO  [root] Processing DIA MS2 (mz range):893.0_896.0( 29/61 )
2021-11-17 15:54:56,121 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:56,121 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:56,392 INFO  [root] 58603 Peak curves found (Memory usage:193MB)
2021-11-17 15:54:56,394 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:56,394 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:56,661 INFO  [root] No of ion clusters:2 (Memory usage:197MB)
2021-11-17 15:54:56,661 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_893_896_PeakCluster.serFS...
2021-11-17 15:54:56,662 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:56,727 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:56,945 INFO  [root] ==================================================================================
2021-11-17 15:54:56,945 INFO  [root] Processing DIA MS2 (mz range):890.0_893.0( 30/61 )
2021-11-17 15:54:56,972 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:56,973 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:57,253 INFO  [root] 65895 Peak curves found (Memory usage:195MB)
2021-11-17 15:54:57,254 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:57,254 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:57,531 INFO  [root] No of ion clusters:7 (Memory usage:201MB)
2021-11-17 15:54:57,532 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_890_893_PeakCluster.serFS...
2021-11-17 15:54:57,532 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:57,589 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:57,783 INFO  [root] ==================================================================================
2021-11-17 15:54:57,783 INFO  [root] Processing DIA MS2 (mz range):887.0_890.0( 31/61 )
2021-11-17 15:54:57,804 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:57,804 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:58,051 INFO  [root] 51049 Peak curves found (Memory usage:191MB)
2021-11-17 15:54:58,053 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:58,053 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:58,312 INFO  [root] No of ion clusters:4 (Memory usage:194MB)
2021-11-17 15:54:58,312 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_887_890_PeakCluster.serFS...
2021-11-17 15:54:58,313 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:58,365 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:58,562 INFO  [root] ==================================================================================
2021-11-17 15:54:58,562 INFO  [root] Processing DIA MS2 (mz range):884.0_887.0( 32/61 )
2021-11-17 15:54:58,583 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:58,583 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:58,834 INFO  [root] 43533 Peak curves found (Memory usage:188MB)
2021-11-17 15:54:58,836 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:58,836 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:59,086 INFO  [root] No of ion clusters:1 (Memory usage:191MB)
2021-11-17 15:54:59,086 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_884_887_PeakCluster.serFS...
2021-11-17 15:54:59,087 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:59,141 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:54:59,342 INFO  [root] ==================================================================================
2021-11-17 15:54:59,342 INFO  [root] Processing DIA MS2 (mz range):881.0_884.0( 33/61 )
2021-11-17 15:54:59,368 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:54:59,368 INFO  [root] Smoothing detected signals......
2021-11-17 15:54:59,589 INFO  [root] 42836 Peak curves found (Memory usage:188MB)
2021-11-17 15:54:59,592 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:54:59,592 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:54:59,846 INFO  [root] No of ion clusters:1 (Memory usage:191MB)
2021-11-17 15:54:59,846 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_881_884_PeakCluster.serFS...
2021-11-17 15:54:59,847 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:54:59,887 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:00,101 INFO  [root] ==================================================================================
2021-11-17 15:55:00,101 INFO  [root] Processing DIA MS2 (mz range):878.0_881.0( 34/61 )
2021-11-17 15:55:00,123 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:00,123 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:00,366 INFO  [root] 41187 Peak curves found (Memory usage:188MB)
2021-11-17 15:55:00,368 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:00,368 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:00,619 INFO  [root] No of ion clusters:5 (Memory usage:191MB)
2021-11-17 15:55:00,620 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_878_881_PeakCluster.serFS...
2021-11-17 15:55:00,620 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:00,661 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:00,871 INFO  [root] ==================================================================================
2021-11-17 15:55:00,871 INFO  [root] Processing DIA MS2 (mz range):875.0_878.0( 35/61 )
2021-11-17 15:55:00,892 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:00,892 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:01,118 INFO  [root] 46443 Peak curves found (Memory usage:190MB)
2021-11-17 15:55:01,120 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:01,120 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:01,379 INFO  [root] No of ion clusters:3 (Memory usage:193MB)
2021-11-17 15:55:01,379 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_875_878_PeakCluster.serFS...
2021-11-17 15:55:01,380 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:01,422 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:01,622 INFO  [root] ==================================================================================
2021-11-17 15:55:01,622 INFO  [root] Processing DIA MS2 (mz range):872.0_875.0( 36/61 )
2021-11-17 15:55:01,645 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:01,646 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:01,928 INFO  [root] 48535 Peak curves found (Memory usage:192MB)
2021-11-17 15:55:01,931 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:01,932 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:02,186 INFO  [root] No of ion clusters:3 (Memory usage:195MB)
2021-11-17 15:55:02,186 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_872_875_PeakCluster.serFS...
2021-11-17 15:55:02,187 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:02,274 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:02,485 INFO  [root] ==================================================================================
2021-11-17 15:55:02,486 INFO  [root] Processing DIA MS2 (mz range):869.0_872.0( 37/61 )
2021-11-17 15:55:02,507 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:02,507 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:02,748 INFO  [root] 50126 Peak curves found (Memory usage:192MB)
2021-11-17 15:55:02,749 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:02,750 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:03,005 INFO  [root] No of ion clusters:6 (Memory usage:196MB)
2021-11-17 15:55:03,005 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_869_872_PeakCluster.serFS...
2021-11-17 15:55:03,006 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:03,052 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:03,257 INFO  [root] ==================================================================================
2021-11-17 15:55:03,257 INFO  [root] Processing DIA MS2 (mz range):866.0_869.0( 38/61 )
2021-11-17 15:55:03,279 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:03,279 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:03,525 INFO  [root] 51342 Peak curves found (Memory usage:193MB)
2021-11-17 15:55:03,527 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:03,527 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:03,793 INFO  [root] No of ion clusters:10 (Memory usage:197MB)
2021-11-17 15:55:03,793 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_866_869_PeakCluster.serFS...
2021-11-17 15:55:03,793 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:03,847 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:04,056 INFO  [root] ==================================================================================
2021-11-17 15:55:04,056 INFO  [root] Processing DIA MS2 (mz range):863.0_866.0( 39/61 )
2021-11-17 15:55:04,079 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:04,079 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:04,335 INFO  [root] 52789 Peak curves found (Memory usage:194MB)
2021-11-17 15:55:04,336 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:04,336 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:04,594 INFO  [root] No of ion clusters:9 (Memory usage:198MB)
2021-11-17 15:55:04,594 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_863_866_PeakCluster.serFS...
2021-11-17 15:55:04,595 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:04,659 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:04,862 INFO  [root] ==================================================================================
2021-11-17 15:55:04,862 INFO  [root] Processing DIA MS2 (mz range):860.0_863.0( 40/61 )
2021-11-17 15:55:04,886 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:04,886 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:05,194 INFO  [root] 53671 Peak curves found (Memory usage:195MB)
2021-11-17 15:55:05,195 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:05,195 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:05,456 INFO  [root] No of ion clusters:6 (Memory usage:199MB)
2021-11-17 15:55:05,456 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_860_863_PeakCluster.serFS...
2021-11-17 15:55:05,457 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:05,521 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:05,738 INFO  [root] ==================================================================================
2021-11-17 15:55:05,738 INFO  [root] Processing DIA MS2 (mz range):857.0_860.0( 41/61 )
2021-11-17 15:55:05,761 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:05,761 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:06,045 INFO  [root] 56886 Peak curves found (Memory usage:196MB)
2021-11-17 15:55:06,047 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:06,047 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:06,331 INFO  [root] No of ion clusters:6 (Memory usage:201MB)
2021-11-17 15:55:06,331 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_857_860_PeakCluster.serFS...
2021-11-17 15:55:06,331 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:06,391 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:06,594 INFO  [root] ==================================================================================
2021-11-17 15:55:06,595 INFO  [root] Processing DIA MS2 (mz range):854.0_857.0( 42/61 )
2021-11-17 15:55:06,623 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:06,624 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:06,945 INFO  [root] 61303 Peak curves found (Memory usage:199MB)
2021-11-17 15:55:06,947 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:06,947 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:07,224 INFO  [root] No of ion clusters:7 (Memory usage:203MB)
2021-11-17 15:55:07,224 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_854_857_PeakCluster.serFS...
2021-11-17 15:55:07,224 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:07,305 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:07,535 INFO  [root] ==================================================================================
2021-11-17 15:55:07,535 INFO  [root] Processing DIA MS2 (mz range):851.0_854.0( 43/61 )
2021-11-17 15:55:07,561 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:07,561 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:07,891 INFO  [root] 65556 Peak curves found (Memory usage:200MB)
2021-11-17 15:55:07,892 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:07,892 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:08,182 INFO  [root] No of ion clusters:5 (Memory usage:205MB)
2021-11-17 15:55:08,183 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_851_854_PeakCluster.serFS...
2021-11-17 15:55:08,184 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:08,247 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:08,454 INFO  [root] ==================================================================================
2021-11-17 15:55:08,454 INFO  [root] Processing DIA MS2 (mz range):848.0_851.0( 44/61 )
2021-11-17 15:55:08,477 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:08,478 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:08,783 INFO  [root] 56169 Peak curves found (Memory usage:197MB)
2021-11-17 15:55:08,784 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:08,785 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:09,067 INFO  [root] No of ion clusters:5 (Memory usage:202MB)
2021-11-17 15:55:09,067 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_848_851_PeakCluster.serFS...
2021-11-17 15:55:09,068 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:09,165 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:09,389 INFO  [root] ==================================================================================
2021-11-17 15:55:09,389 INFO  [root] Processing DIA MS2 (mz range):845.0_848.0( 45/61 )
2021-11-17 15:55:09,416 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:09,416 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:09,707 INFO  [root] 56755 Peak curves found (Memory usage:198MB)
2021-11-17 15:55:09,709 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:09,709 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:09,985 INFO  [root] No of ion clusters:5 (Memory usage:202MB)
2021-11-17 15:55:09,985 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_845_848_PeakCluster.serFS...
2021-11-17 15:55:09,986 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:10,061 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:10,270 INFO  [root] ==================================================================================
2021-11-17 15:55:10,270 INFO  [root] Processing DIA MS2 (mz range):842.0_845.0( 46/61 )
2021-11-17 15:55:10,295 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:10,295 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:10,578 INFO  [root] 54787 Peak curves found (Memory usage:197MB)
2021-11-17 15:55:10,579 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:10,579 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:10,852 INFO  [root] No of ion clusters:7 (Memory usage:202MB)
2021-11-17 15:55:10,852 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_842_845_PeakCluster.serFS...
2021-11-17 15:55:10,853 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:10,928 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:11,134 INFO  [root] ==================================================================================
2021-11-17 15:55:11,134 INFO  [root] Processing DIA MS2 (mz range):839.0_842.0( 47/61 )
2021-11-17 15:55:11,158 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:11,158 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:11,482 INFO  [root] 56291 Peak curves found (Memory usage:198MB)
2021-11-17 15:55:11,484 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:11,484 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:11,761 INFO  [root] No of ion clusters:1 (Memory usage:203MB)
2021-11-17 15:55:11,761 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_839_842_PeakCluster.serFS...
2021-11-17 15:55:11,762 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:11,865 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:12,071 INFO  [root] ==================================================================================
2021-11-17 15:55:12,071 INFO  [root] Processing DIA MS2 (mz range):836.0_839.0( 48/61 )
2021-11-17 15:55:12,098 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:12,098 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:12,407 INFO  [root] 62614 Peak curves found (Memory usage:201MB)
2021-11-17 15:55:12,409 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:12,409 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:12,688 INFO  [root] No of ion clusters:7 (Memory usage:206MB)
2021-11-17 15:55:12,688 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_836_839_PeakCluster.serFS...
2021-11-17 15:55:12,689 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:12,778 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:12,984 INFO  [root] ==================================================================================
2021-11-17 15:55:12,984 INFO  [root] Processing DIA MS2 (mz range):833.0_836.0( 49/61 )
2021-11-17 15:55:13,010 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:13,011 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:13,293 INFO  [root] 59481 Peak curves found (Memory usage:200MB)
2021-11-17 15:55:13,295 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:13,295 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:13,566 INFO  [root] No of ion clusters:7 (Memory usage:205MB)
2021-11-17 15:55:13,566 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_833_836_PeakCluster.serFS...
2021-11-17 15:55:13,567 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:13,651 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:13,871 INFO  [root] ==================================================================================
2021-11-17 15:55:13,871 INFO  [root] Processing DIA MS2 (mz range):830.0_833.0( 50/61 )
2021-11-17 15:55:13,903 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:13,903 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:14,275 INFO  [root] 67176 Peak curves found (Memory usage:204MB)
2021-11-17 15:55:14,277 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:14,277 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:14,581 INFO  [root] No of ion clusters:6 (Memory usage:209MB)
2021-11-17 15:55:14,581 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_830_833_PeakCluster.serFS...
2021-11-17 15:55:14,582 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:14,667 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:14,893 INFO  [root] ==================================================================================
2021-11-17 15:55:14,893 INFO  [root] Processing DIA MS2 (mz range):827.0_830.0( 51/61 )
2021-11-17 15:55:14,921 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:14,921 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:15,254 INFO  [root] 72485 Peak curves found (Memory usage:206MB)
2021-11-17 15:55:15,256 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:15,256 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:15,549 INFO  [root] No of ion clusters:5 (Memory usage:212MB)
2021-11-17 15:55:15,549 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_827_830_PeakCluster.serFS...
2021-11-17 15:55:15,550 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:15,650 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:15,888 INFO  [root] ==================================================================================
2021-11-17 15:55:15,888 INFO  [root] Processing DIA MS2 (mz range):824.0_827.0( 52/61 )
2021-11-17 15:55:15,916 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:15,916 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:16,272 INFO  [root] 77476 Peak curves found (Memory usage:208MB)
2021-11-17 15:55:16,274 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:16,274 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:16,567 INFO  [root] No of ion clusters:2 (Memory usage:214MB)
2021-11-17 15:55:16,567 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_824_827_PeakCluster.serFS...
2021-11-17 15:55:16,568 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:16,664 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:16,881 INFO  [root] ==================================================================================
2021-11-17 15:55:16,881 INFO  [root] Processing DIA MS2 (mz range):821.0_824.0( 53/61 )
2021-11-17 15:55:16,913 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:16,913 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:17,335 INFO  [root] 87072 Peak curves found (Memory usage:213MB)
2021-11-17 15:55:17,337 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:17,337 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:17,646 INFO  [root] No of ion clusters:6 (Memory usage:220MB)
2021-11-17 15:55:17,646 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_821_824_PeakCluster.serFS...
2021-11-17 15:55:17,647 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:17,769 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:17,994 INFO  [root] ==================================================================================
2021-11-17 15:55:17,994 INFO  [root] Processing DIA MS2 (mz range):818.0_821.0( 54/61 )
2021-11-17 15:55:18,024 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:18,024 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:18,435 INFO  [root] 82633 Peak curves found (Memory usage:212MB)
2021-11-17 15:55:18,437 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:18,437 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:18,734 INFO  [root] No of ion clusters:6 (Memory usage:218MB)
2021-11-17 15:55:18,734 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_818_821_PeakCluster.serFS...
2021-11-17 15:55:18,734 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:18,906 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:19,098 INFO  [root] ==================================================================================
2021-11-17 15:55:19,098 INFO  [root] Processing DIA MS2 (mz range):815.0_818.0( 55/61 )
2021-11-17 15:55:19,127 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:19,127 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:19,516 INFO  [root] 79539 Peak curves found (Memory usage:210MB)
2021-11-17 15:55:19,518 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:19,518 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:19,826 INFO  [root] No of ion clusters:3 (Memory usage:216MB)
2021-11-17 15:55:19,826 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_815_818_PeakCluster.serFS...
2021-11-17 15:55:19,826 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:19,939 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:20,145 INFO  [root] ==================================================================================
2021-11-17 15:55:20,145 INFO  [root] Processing DIA MS2 (mz range):812.0_815.0( 56/61 )
2021-11-17 15:55:20,173 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:20,173 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:20,550 INFO  [root] 71876 Peak curves found (Memory usage:207MB)
2021-11-17 15:55:20,552 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:20,552 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:20,863 INFO  [root] No of ion clusters:6 (Memory usage:213MB)
2021-11-17 15:55:20,863 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_812_815_PeakCluster.serFS...
2021-11-17 15:55:20,864 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:20,977 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:21,185 INFO  [root] ==================================================================================
2021-11-17 15:55:21,185 INFO  [root] Processing DIA MS2 (mz range):809.0_812.0( 57/61 )
2021-11-17 15:55:21,211 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:21,211 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:21,581 INFO  [root] 70412 Peak curves found (Memory usage:207MB)
2021-11-17 15:55:21,583 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:21,583 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:21,909 INFO  [root] No of ion clusters:10 (Memory usage:212MB)
2021-11-17 15:55:21,909 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_809_812_PeakCluster.serFS...
2021-11-17 15:55:21,910 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:22,035 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:22,249 INFO  [root] ==================================================================================
2021-11-17 15:55:22,249 INFO  [root] Processing DIA MS2 (mz range):806.0_809.0( 58/61 )
2021-11-17 15:55:22,276 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:22,276 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:22,647 INFO  [root] 71867 Peak curves found (Memory usage:208MB)
2021-11-17 15:55:22,649 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:22,649 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:22,952 INFO  [root] No of ion clusters:7 (Memory usage:214MB)
2021-11-17 15:55:22,953 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_806_809_PeakCluster.serFS...
2021-11-17 15:55:22,953 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:23,093 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:23,304 INFO  [root] ==================================================================================
2021-11-17 15:55:23,304 INFO  [root] Processing DIA MS2 (mz range):803.0_806.0( 59/61 )
2021-11-17 15:55:23,333 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:23,333 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:23,676 INFO  [root] 71637 Peak curves found (Memory usage:209MB)
2021-11-17 15:55:23,678 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:23,678 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:23,968 INFO  [root] No of ion clusters:3 (Memory usage:214MB)
2021-11-17 15:55:23,968 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_803_806_PeakCluster.serFS...
2021-11-17 15:55:23,969 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:24,089 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:24,300 INFO  [root] ==================================================================================
2021-11-17 15:55:24,301 INFO  [root] Processing DIA MS2 (mz range):800.0_803.0( 60/61 )
2021-11-17 15:55:24,322 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:24,322 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:24,632 INFO  [root] 37141 Peak curves found (Memory usage:196MB)
2021-11-17 15:55:24,634 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:24,634 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:24,879 INFO  [root] No of ion clusters:3 (Memory usage:199MB)
2021-11-17 15:55:24,879 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_800_803_PeakCluster.serFS...
2021-11-17 15:55:24,880 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:24,993 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:25,200 INFO  [root] ==================================================================================
2021-11-17 15:55:25,200 INFO  [root] Processing DIA MS2 (mz range):797.0_800.0( 61/61 )
2021-11-17 15:55:25,214 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:25,214 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:25,615 INFO  [root] 36170 Peak curves found (Memory usage:198MB)
2021-11-17 15:55:25,617 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:25,617 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:25,858 INFO  [root] No of ion clusters:31 (Memory usage:201MB)
2021-11-17 15:55:25,858 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_797_800_PeakCluster.serFS...
2021-11-17 15:55:25,859 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:55:26,242 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:55:26,536 INFO  [root] ==================================================================================
2021-11-17 15:55:27,389 INFO  [root] C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.mzXML processed time:0 hour, 1 min, 12 sec
2021-11-17 15:55:27,389 INFO  [root] Job complete
2021-11-17 15:55:27,389 INFO  [root] =================================================================================================
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -Xmx25G -Dlibs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\DIA_Umpire_SE-2.2.3.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar" dia_umpire_se.DIA_Umpire_SE C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.mzXML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
=================================================================================================
DIA-Umpire singal extraction analysis  (version: v2.2.3)
(c) University of Michigan
2021-11-17 15:55:34,744 INFO  [root] Version: v2.2.3
2021-11-17 15:55:34,745 INFO  [root] Parameter file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\umpire-se.params
2021-11-17 15:55:34,745 INFO  [root] Spectra file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.mzXML
2021-11-17 15:55:34,747 INFO  [root] 
2021-11-17 15:55:34,747 INFO  [root] ####################################################################################################
2021-11-17 15:55:34,747 INFO  [root] #No of threads
2021-11-17 15:55:34,747 INFO  [root] Thread = 7
2021-11-17 15:55:34,747 INFO  [root] ####################################################################################################
2021-11-17 15:55:34,748 INFO  [root] 
2021-11-17 15:55:34,748 INFO  [root] ## omit Thread
2021-11-17 15:55:34,748 INFO  [root] 
2021-11-17 15:55:34,748 INFO  [root] #Precursor-fragments grouping parameters
2021-11-17 15:55:34,748 INFO  [root] RPmax = 25
2021-11-17 15:55:34,748 INFO  [root] RFmax = 500
2021-11-17 15:55:34,748 INFO  [root] CorrThreshold = 0
2021-11-17 15:55:34,749 INFO  [root] DeltaApex = 0.2
2021-11-17 15:55:34,749 INFO  [root] RTOverlap = 0.3
2021-11-17 15:55:34,749 INFO  [root] 
2021-11-17 15:55:34,749 INFO  [root] #Fragment intensity adjustments
2021-11-17 15:55:34,749 INFO  [root] # change BoostComplementaryIon if later using database search results to build libraries for Skyline/OpenSWATH
2021-11-17 15:55:34,749 INFO  [root] AdjustFragIntensity = true
2021-11-17 15:55:34,749 INFO  [root] BoostComplementaryIon = false
2021-11-17 15:55:34,749 INFO  [root] 
2021-11-17 15:55:34,749 INFO  [root] #Export detected MS1 features (output feature file can be loaded and mapped to RAW data in BatMass)
2021-11-17 15:55:34,749 INFO  [root] ExportPrecursorPeak = false
2021-11-17 15:55:34,749 INFO  [root] 
2021-11-17 15:55:34,749 INFO  [root] Q1 = true
2021-11-17 15:55:34,749 INFO  [root] Q2 = true
2021-11-17 15:55:34,749 INFO  [root] Q3 = true
2021-11-17 15:55:34,750 INFO  [root] 
2021-11-17 15:55:34,750 INFO  [root] #Signal extraction: mass accuracy and resolution
2021-11-17 15:55:34,750 INFO  [root] # resolution parameter matters only for data generated in profile mode
2021-11-17 15:55:34,750 INFO  [root] SE.MS1PPM = 10
2021-11-17 15:55:34,750 INFO  [root] SE.MS2PPM = 10
2021-11-17 15:55:34,750 INFO  [root] SE.Resolution = 60000
2021-11-17 15:55:34,750 INFO  [root] 
2021-11-17 15:55:34,750 INFO  [root] #Signal extraction: signal to noise filter
2021-11-17 15:55:34,750 INFO  [root] SE.SN = 1.1
2021-11-17 15:55:34,750 INFO  [root] SE.MS2SN = 1.1
2021-11-17 15:55:34,750 INFO  [root] 
2021-11-17 15:55:34,750 INFO  [root] #Signal extraction: minimum signal intensity filter
2021-11-17 15:55:34,750 INFO  [root] # for Thermo data, filtering is usually not necessary. Set SE.EstimateBG to false and SE.MinMSIntensity and SE.MinMSMSIntensity to a low value, e.g. 1
2021-11-17 15:55:34,750 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.EstimateBG to yes (or apply SE.MinMSIntensity and SE.MinMSMSIntensity values based on BatMass visualization)
2021-11-17 15:55:34,750 INFO  [root] SE.EstimateBG = false
2021-11-17 15:55:34,750 INFO  [root] SE.MinMSIntensity = 1
2021-11-17 15:55:34,750 INFO  [root] SE.MinMSMSIntensity = 1
2021-11-17 15:55:34,751 INFO  [root] 
2021-11-17 15:55:34,751 INFO  [root] #Signal extraction: peak curve detection and isotope grouping
2021-11-17 15:55:34,751 INFO  [root] # for older Q Exactive data, or when too many MS1 features are extracted, set SE.NoMissedScan to 1
2021-11-17 15:55:34,751 INFO  [root] SE.NoMissedScan = 1
2021-11-17 15:55:34,751 INFO  [root] SE.MaxCurveRTRange = 2
2021-11-17 15:55:34,751 INFO  [root] SE.RemoveGroupedPeaks = true
2021-11-17 15:55:34,751 INFO  [root] SE.RemoveGroupedPeaksRTOverlap = 0.3
2021-11-17 15:55:34,751 INFO  [root] SE.RemoveGroupedPeaksCorr = 0.3
2021-11-17 15:55:34,751 INFO  [root] SE.MinNoPeakCluster = 2
2021-11-17 15:55:34,751 INFO  [root] SE.MaxNoPeakCluster = 4
2021-11-17 15:55:34,751 INFO  [root] 
2021-11-17 15:55:34,751 INFO  [root] #Signal extraction: filtering of MS1 features
2021-11-17 15:55:34,751 INFO  [root] # if interested in modified peptides, increase MassDefectOffset parameter, or set SE.MassDefectFilter to false
2021-11-17 15:55:34,751 INFO  [root] SE.IsoPattern = 0.3
2021-11-17 15:55:34,751 INFO  [root] SE.MassDefectFilter = false
2021-11-17 15:55:34,751 INFO  [root] SE.MassDefectOffset = 0.1
2021-11-17 15:55:34,752 INFO  [root] 
2021-11-17 15:55:34,752 INFO  [root] #Signal extraction: other
2021-11-17 15:55:34,752 INFO  [root] SE.StartCharge = 1
2021-11-17 15:55:34,752 INFO  [root] SE.EndCharge = 5
2021-11-17 15:55:34,752 INFO  [root] SE.MS2StartCharge = 2
2021-11-17 15:55:34,752 INFO  [root] SE.MS2EndCharge = 5
2021-11-17 15:55:34,951 INFO  [root] SE.MinFrag = 10
2021-11-17 15:55:34,951 INFO  [root] SE.StartRT = 0
2021-11-17 15:55:34,951 INFO  [root] SE.EndRT = 9999
2021-11-17 15:55:34,952 INFO  [root] SE.MinMZ = 200
2021-11-17 15:55:34,952 INFO  [root] SE.MinPrecursorMass = 600
2021-11-17 15:55:34,952 INFO  [root] SE.MaxPrecursorMass = 5000
2021-11-17 15:55:34,952 INFO  [root] 
2021-11-17 15:55:34,952 INFO  [root] 
2021-11-17 15:55:34,952 INFO  [root] #Isolation window setting
2021-11-17 15:55:34,952 INFO  [root] #The current version supports the following window type: SWATH (fixed window size), V_SWATH (variable SWATH window), MSX, MSE, pSMART
2021-11-17 15:55:34,952 INFO  [root] WindowType = SWATH
2021-11-17 15:55:34,953 INFO  [root] 
2021-11-17 15:55:34,953 INFO  [root] #Fix window size (For SWATH)
2021-11-17 15:55:34,953 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:55:34,953 INFO  [root] WindowSize = 10
2021-11-17 15:55:34,953 INFO  [root] 
2021-11-17 15:55:34,953 INFO  [root] #Variable SWATH window setting (start m/z, end m/z, separated by Tab)
2021-11-17 15:55:34,953 INFO  [root] # for Thermo data, this will be determined from raw data automatically
2021-11-17 15:55:34,953 INFO  [root] ==window setting begin
2021-11-17 15:55:34,953 INFO  [root] 
2021-11-17 15:55:34,954 INFO  [root] =================================================================================================
2021-11-17 15:55:34,954 INFO  [root] Processing C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.mzXML....
2021-11-17 15:55:34,964 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_diasetting.ser...
2021-11-17 15:55:34,977 INFO  [root] Writing parameter to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_params.ser...
2021-11-17 15:55:34,979 INFO  [root] Module A: Signal extraction
2021-11-17 15:55:38,124 INFO  [root] Writing DIA setting to file:C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_diasetting.ser...
2021-11-17 15:55:38,689 INFO  [root] Processing MS1 peak detection
2021-11-17 15:55:38,690 INFO  [root] MS1 average cycle time : 2.6801202 seconds
2021-11-17 15:55:42,148 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:42,148 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:45,814 INFO  [root] 426342 Peak curves found (Memory usage:294MB)
2021-11-17 15:55:45,814 INFO  [root] Inclusion mz values found: 0/0
2021-11-17 15:55:45,814 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:45,815 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:55:58,635 INFO  [root] No of ion clusters:26735 (Memory usage:238MB)
2021-11-17 15:55:58,651 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_PeakCluster.serFS...
2021-11-17 15:55:58,926 INFO  [root] ==================================================================================
2021-11-17 15:55:58,926 INFO  [root] Processing DIA MS2 (mz range):977.0_980.0( 1/61 )
2021-11-17 15:55:58,997 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:55:58,997 INFO  [root] Smoothing detected signals......
2021-11-17 15:55:59,859 INFO  [root] 55799 Peak curves found (Memory usage:276MB)
2021-11-17 15:55:59,864 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:55:59,864 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:00,255 INFO  [root] No of ion clusters:23 (Memory usage:281MB)
2021-11-17 15:56:00,256 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_977_980_PeakCluster.serFS...
2021-11-17 15:56:00,257 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:00,862 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:01,512 INFO  [root] ==================================================================================
2021-11-17 15:56:01,512 INFO  [root] Processing DIA MS2 (mz range):974.0_977.0( 2/61 )
2021-11-17 15:56:01,571 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:01,571 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:02,225 INFO  [root] 63339 Peak curves found (Memory usage:266MB)
2021-11-17 15:56:02,228 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:02,229 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:02,601 INFO  [root] No of ion clusters:6 (Memory usage:271MB)
2021-11-17 15:56:02,601 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_974_977_PeakCluster.serFS...
2021-11-17 15:56:02,602 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:02,748 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:03,097 INFO  [root] ==================================================================================
2021-11-17 15:56:03,097 INFO  [root] Processing DIA MS2 (mz range):971.0_974.0( 3/61 )
2021-11-17 15:56:03,149 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:03,149 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:03,707 INFO  [root] 104538 Peak curves found (Memory usage:284MB)
2021-11-17 15:56:03,709 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:03,709 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:04,150 INFO  [root] No of ion clusters:4 (Memory usage:292MB)
2021-11-17 15:56:04,150 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_971_974_PeakCluster.serFS...
2021-11-17 15:56:04,150 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:04,415 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:04,758 INFO  [root] ==================================================================================
2021-11-17 15:56:04,758 INFO  [root] Processing DIA MS2 (mz range):968.0_971.0( 4/61 )
2021-11-17 15:56:04,799 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:04,799 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:05,286 INFO  [root] 96056 Peak curves found (Memory usage:280MB)
2021-11-17 15:56:05,288 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:05,288 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:05,809 INFO  [root] No of ion clusters:9 (Memory usage:288MB)
2021-11-17 15:56:05,809 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_968_971_PeakCluster.serFS...
2021-11-17 15:56:05,810 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:05,969 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:06,321 INFO  [root] ==================================================================================
2021-11-17 15:56:06,321 INFO  [root] Processing DIA MS2 (mz range):965.0_968.0( 5/61 )
2021-11-17 15:56:06,358 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:06,358 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:06,785 INFO  [root] 96126 Peak curves found (Memory usage:281MB)
2021-11-17 15:56:06,787 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:06,787 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:07,246 INFO  [root] No of ion clusters:5 (Memory usage:289MB)
2021-11-17 15:56:07,247 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_965_968_PeakCluster.serFS...
2021-11-17 15:56:07,247 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:07,403 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:07,728 INFO  [root] ==================================================================================
2021-11-17 15:56:07,728 INFO  [root] Processing DIA MS2 (mz range):962.0_965.0( 6/61 )
2021-11-17 15:56:07,783 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:07,784 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:08,506 INFO  [root] 114564 Peak curves found (Memory usage:290MB)
2021-11-17 15:56:08,510 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:08,510 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:09,029 INFO  [root] No of ion clusters:11 (Memory usage:299MB)
2021-11-17 15:56:09,029 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_962_965_PeakCluster.serFS...
2021-11-17 15:56:09,030 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:09,271 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:09,622 INFO  [root] ==================================================================================
2021-11-17 15:56:09,622 INFO  [root] Processing DIA MS2 (mz range):959.0_962.0( 7/61 )
2021-11-17 15:56:09,667 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:09,667 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:10,415 INFO  [root] 119574 Peak curves found (Memory usage:294MB)
2021-11-17 15:56:10,417 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:10,417 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:10,938 INFO  [root] No of ion clusters:6 (Memory usage:303MB)
2021-11-17 15:56:10,938 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_959_962_PeakCluster.serFS...
2021-11-17 15:56:10,939 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:11,183 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:11,506 INFO  [root] ==================================================================================
2021-11-17 15:56:11,506 INFO  [root] Processing DIA MS2 (mz range):956.0_959.0( 8/61 )
2021-11-17 15:56:11,552 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:11,552 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:12,274 INFO  [root] 132028 Peak curves found (Memory usage:299MB)
2021-11-17 15:56:12,276 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:12,276 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:12,759 INFO  [root] No of ion clusters:4 (Memory usage:309MB)
2021-11-17 15:56:12,759 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_956_959_PeakCluster.serFS...
2021-11-17 15:56:12,760 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:13,058 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:13,358 INFO  [root] ==================================================================================
2021-11-17 15:56:13,358 INFO  [root] Processing DIA MS2 (mz range):953.0_956.0( 9/61 )
2021-11-17 15:56:13,400 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:13,400 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:14,289 INFO  [root] 128212 Peak curves found (Memory usage:299MB)
2021-11-17 15:56:14,291 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:14,291 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:14,782 INFO  [root] No of ion clusters:15 (Memory usage:309MB)
2021-11-17 15:56:14,782 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_953_956_PeakCluster.serFS...
2021-11-17 15:56:14,783 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:14,982 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:15,314 INFO  [root] ==================================================================================
2021-11-17 15:56:15,314 INFO  [root] Processing DIA MS2 (mz range):950.0_953.0( 10/61 )
2021-11-17 15:56:15,362 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:15,362 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:16,171 INFO  [root] 129182 Peak curves found (Memory usage:300MB)
2021-11-17 15:56:16,173 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:16,173 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:16,644 INFO  [root] No of ion clusters:12 (Memory usage:310MB)
2021-11-17 15:56:16,644 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_950_953_PeakCluster.serFS...
2021-11-17 15:56:16,645 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:16,833 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:17,172 INFO  [root] ==================================================================================
2021-11-17 15:56:17,173 INFO  [root] Processing DIA MS2 (mz range):947.0_950.0( 11/61 )
2021-11-17 15:56:17,211 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:17,211 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:17,796 INFO  [root] 111109 Peak curves found (Memory usage:294MB)
2021-11-17 15:56:17,798 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:17,798 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:18,282 INFO  [root] No of ion clusters:12 (Memory usage:303MB)
2021-11-17 15:56:18,282 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_947_950_PeakCluster.serFS...
2021-11-17 15:56:18,283 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:18,488 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:18,813 INFO  [root] ==================================================================================
2021-11-17 15:56:18,814 INFO  [root] Processing DIA MS2 (mz range):944.0_947.0( 12/61 )
2021-11-17 15:56:18,848 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:18,848 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:19,382 INFO  [root] 100522 Peak curves found (Memory usage:290MB)
2021-11-17 15:56:19,384 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:19,384 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:19,814 INFO  [root] No of ion clusters:12 (Memory usage:298MB)
2021-11-17 15:56:19,814 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_944_947_PeakCluster.serFS...
2021-11-17 15:56:19,815 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:19,954 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:20,273 INFO  [root] ==================================================================================
2021-11-17 15:56:20,273 INFO  [root] Processing DIA MS2 (mz range):941.0_944.0( 13/61 )
2021-11-17 15:56:20,308 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:20,308 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:20,763 INFO  [root] 91347 Peak curves found (Memory usage:287MB)
2021-11-17 15:56:20,765 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:20,765 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:21,176 INFO  [root] No of ion clusters:9 (Memory usage:294MB)
2021-11-17 15:56:21,176 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_941_944_PeakCluster.serFS...
2021-11-17 15:56:21,177 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:21,295 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:21,600 INFO  [root] ==================================================================================
2021-11-17 15:56:21,600 INFO  [root] Processing DIA MS2 (mz range):938.0_941.0( 14/61 )
2021-11-17 15:56:21,631 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:21,631 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:22,095 INFO  [root] 92115 Peak curves found (Memory usage:288MB)
2021-11-17 15:56:22,097 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:22,097 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:22,519 INFO  [root] No of ion clusters:7 (Memory usage:295MB)
2021-11-17 15:56:22,519 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_938_941_PeakCluster.serFS...
2021-11-17 15:56:22,520 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:22,643 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:22,971 INFO  [root] ==================================================================================
2021-11-17 15:56:22,971 INFO  [root] Processing DIA MS2 (mz range):935.0_938.0( 15/61 )
2021-11-17 15:56:23,006 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:23,006 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:23,466 INFO  [root] 90427 Peak curves found (Memory usage:288MB)
2021-11-17 15:56:23,467 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:23,467 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:23,874 INFO  [root] No of ion clusters:11 (Memory usage:295MB)
2021-11-17 15:56:23,874 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_935_938_PeakCluster.serFS...
2021-11-17 15:56:23,875 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:24,001 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:24,307 INFO  [root] ==================================================================================
2021-11-17 15:56:24,307 INFO  [root] Processing DIA MS2 (mz range):932.0_935.0( 16/61 )
2021-11-17 15:56:24,341 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:24,341 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:24,792 INFO  [root] 95297 Peak curves found (Memory usage:290MB)
2021-11-17 15:56:24,794 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:24,794 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:25,212 INFO  [root] No of ion clusters:14 (Memory usage:298MB)
2021-11-17 15:56:25,212 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_932_935_PeakCluster.serFS...
2021-11-17 15:56:25,213 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:25,321 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:25,642 INFO  [root] ==================================================================================
2021-11-17 15:56:25,642 INFO  [root] Processing DIA MS2 (mz range):929.0_932.0( 17/61 )
2021-11-17 15:56:25,675 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:25,675 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:26,152 INFO  [root] 93848 Peak curves found (Memory usage:291MB)
2021-11-17 15:56:26,154 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:26,154 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:26,586 INFO  [root] No of ion clusters:9 (Memory usage:298MB)
2021-11-17 15:56:26,587 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_929_932_PeakCluster.serFS...
2021-11-17 15:56:26,587 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:26,745 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:27,058 INFO  [root] ==================================================================================
2021-11-17 15:56:27,058 INFO  [root] Processing DIA MS2 (mz range):926.0_929.0( 18/61 )
2021-11-17 15:56:27,090 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:27,090 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:27,559 INFO  [root] 90593 Peak curves found (Memory usage:290MB)
2021-11-17 15:56:27,561 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:27,561 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:27,997 INFO  [root] No of ion clusters:5 (Memory usage:297MB)
2021-11-17 15:56:27,998 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_926_929_PeakCluster.serFS...
2021-11-17 15:56:27,998 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:28,102 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:28,413 INFO  [root] ==================================================================================
2021-11-17 15:56:28,413 INFO  [root] Processing DIA MS2 (mz range):923.0_926.0( 19/61 )
2021-11-17 15:56:28,441 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:28,441 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:28,822 INFO  [root] 77486 Peak curves found (Memory usage:286MB)
2021-11-17 15:56:28,824 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:28,824 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:29,222 INFO  [root] No of ion clusters:13 (Memory usage:292MB)
2021-11-17 15:56:29,222 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_923_926_PeakCluster.serFS...
2021-11-17 15:56:29,222 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:29,322 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:29,648 INFO  [root] ==================================================================================
2021-11-17 15:56:29,648 INFO  [root] Processing DIA MS2 (mz range):920.0_923.0( 20/61 )
2021-11-17 15:56:29,680 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:29,680 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:30,116 INFO  [root] 92970 Peak curves found (Memory usage:292MB)
2021-11-17 15:56:30,118 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:30,118 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:30,536 INFO  [root] No of ion clusters:6 (Memory usage:299MB)
2021-11-17 15:56:30,536 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_920_923_PeakCluster.serFS...
2021-11-17 15:56:30,537 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:30,630 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:30,932 INFO  [root] ==================================================================================
2021-11-17 15:56:30,933 INFO  [root] Processing DIA MS2 (mz range):917.0_920.0( 21/61 )
2021-11-17 15:56:30,968 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:30,968 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:31,507 INFO  [root] 91790 Peak curves found (Memory usage:293MB)
2021-11-17 15:56:31,509 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:31,509 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:31,922 INFO  [root] No of ion clusters:9 (Memory usage:300MB)
2021-11-17 15:56:31,922 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_917_920_PeakCluster.serFS...
2021-11-17 15:56:31,923 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:32,075 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:32,380 INFO  [root] ==================================================================================
2021-11-17 15:56:32,380 INFO  [root] Processing DIA MS2 (mz range):914.0_917.0( 22/61 )
2021-11-17 15:56:32,410 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:32,410 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:32,826 INFO  [root] 88853 Peak curves found (Memory usage:291MB)
2021-11-17 15:56:32,828 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:32,828 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:33,272 INFO  [root] No of ion clusters:11 (Memory usage:298MB)
2021-11-17 15:56:33,272 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_914_917_PeakCluster.serFS...
2021-11-17 15:56:33,273 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:33,363 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:33,662 INFO  [root] ==================================================================================
2021-11-17 15:56:33,662 INFO  [root] Processing DIA MS2 (mz range):911.0_914.0( 23/61 )
2021-11-17 15:56:33,691 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:33,692 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:34,078 INFO  [root] 79945 Peak curves found (Memory usage:288MB)
2021-11-17 15:56:34,080 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:34,080 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:34,464 INFO  [root] No of ion clusters:13 (Memory usage:295MB)
2021-11-17 15:56:34,464 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_911_914_PeakCluster.serFS...
2021-11-17 15:56:34,465 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:34,562 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:34,867 INFO  [root] ==================================================================================
2021-11-17 15:56:34,867 INFO  [root] Processing DIA MS2 (mz range):908.0_911.0( 24/61 )
2021-11-17 15:56:34,897 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:34,897 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:35,293 INFO  [root] 86398 Peak curves found (Memory usage:291MB)
2021-11-17 15:56:35,295 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:35,295 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:35,711 INFO  [root] No of ion clusters:15 (Memory usage:298MB)
2021-11-17 15:56:35,711 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_908_911_PeakCluster.serFS...
2021-11-17 15:56:35,711 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:35,812 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:36,161 INFO  [root] ==================================================================================
2021-11-17 15:56:36,161 INFO  [root] Processing DIA MS2 (mz range):905.0_908.0( 25/61 )
2021-11-17 15:56:36,190 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:36,190 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:36,586 INFO  [root] 89730 Peak curves found (Memory usage:293MB)
2021-11-17 15:56:36,588 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:36,588 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:36,993 INFO  [root] No of ion clusters:14 (Memory usage:300MB)
2021-11-17 15:56:36,993 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_905_908_PeakCluster.serFS...
2021-11-17 15:56:36,994 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:37,114 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:37,428 INFO  [root] ==================================================================================
2021-11-17 15:56:37,428 INFO  [root] Processing DIA MS2 (mz range):902.0_905.0( 26/61 )
2021-11-17 15:56:37,456 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:37,456 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:37,833 INFO  [root] 79597 Peak curves found (Memory usage:289MB)
2021-11-17 15:56:37,834 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:37,834 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:38,246 INFO  [root] No of ion clusters:13 (Memory usage:296MB)
2021-11-17 15:56:38,246 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_902_905_PeakCluster.serFS...
2021-11-17 15:56:38,247 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:38,323 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:38,629 INFO  [root] ==================================================================================
2021-11-17 15:56:38,629 INFO  [root] Processing DIA MS2 (mz range):899.0_902.0( 27/61 )
2021-11-17 15:56:38,660 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:38,660 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:39,094 INFO  [root] 85636 Peak curves found (Memory usage:293MB)
2021-11-17 15:56:39,096 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:39,096 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:39,494 INFO  [root] No of ion clusters:5 (Memory usage:299MB)
2021-11-17 15:56:39,494 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_899_902_PeakCluster.serFS...
2021-11-17 15:56:39,495 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:39,585 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:39,890 INFO  [root] ==================================================================================
2021-11-17 15:56:39,890 INFO  [root] Processing DIA MS2 (mz range):896.0_899.0( 28/61 )
2021-11-17 15:56:39,926 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:39,926 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:40,421 INFO  [root] 111818 Peak curves found (Memory usage:304MB)
2021-11-17 15:56:40,422 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:40,422 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:40,879 INFO  [root] No of ion clusters:13 (Memory usage:312MB)
2021-11-17 15:56:40,879 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_896_899_PeakCluster.serFS...
2021-11-17 15:56:40,880 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:41,149 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:41,468 INFO  [root] ==================================================================================
2021-11-17 15:56:41,468 INFO  [root] Processing DIA MS2 (mz range):893.0_896.0( 29/61 )
2021-11-17 15:56:41,506 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:41,506 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:42,033 INFO  [root] 117307 Peak curves found (Memory usage:307MB)
2021-11-17 15:56:42,034 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:42,034 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:42,385 INFO  [root] No of ion clusters:13 (Memory usage:314MB)
2021-11-17 15:56:42,386 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_893_896_PeakCluster.serFS...
2021-11-17 15:56:42,386 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:42,575 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:42,891 INFO  [root] ==================================================================================
2021-11-17 15:56:42,891 INFO  [root] Processing DIA MS2 (mz range):890.0_893.0( 30/61 )
2021-11-17 15:56:42,934 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:42,934 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:43,395 INFO  [root] 108543 Peak curves found (Memory usage:302MB)
2021-11-17 15:56:43,398 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:43,398 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:43,843 INFO  [root] No of ion clusters:9 (Memory usage:310MB)
2021-11-17 15:56:43,843 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_890_893_PeakCluster.serFS...
2021-11-17 15:56:43,844 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:44,061 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:44,457 INFO  [root] ==================================================================================
2021-11-17 15:56:44,457 INFO  [root] Processing DIA MS2 (mz range):887.0_890.0( 31/61 )
2021-11-17 15:56:44,492 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:44,492 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:44,997 INFO  [root] 99110 Peak curves found (Memory usage:299MB)
2021-11-17 15:56:44,999 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:44,999 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:45,436 INFO  [root] No of ion clusters:10 (Memory usage:306MB)
2021-11-17 15:56:45,436 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_887_890_PeakCluster.serFS...
2021-11-17 15:56:45,436 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:45,635 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:45,954 INFO  [root] ==================================================================================
2021-11-17 15:56:45,954 INFO  [root] Processing DIA MS2 (mz range):884.0_887.0( 32/61 )
2021-11-17 15:56:45,986 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:45,986 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:46,392 INFO  [root] 89549 Peak curves found (Memory usage:295MB)
2021-11-17 15:56:46,393 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:46,393 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:46,800 INFO  [root] No of ion clusters:5 (Memory usage:302MB)
2021-11-17 15:56:46,800 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_884_887_PeakCluster.serFS...
2021-11-17 15:56:46,801 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:46,903 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:47,204 INFO  [root] ==================================================================================
2021-11-17 15:56:47,204 INFO  [root] Processing DIA MS2 (mz range):881.0_884.0( 33/61 )
2021-11-17 15:56:47,249 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:47,249 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:47,644 INFO  [root] 79778 Peak curves found (Memory usage:292MB)
2021-11-17 15:56:47,646 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:47,646 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:48,034 INFO  [root] No of ion clusters:9 (Memory usage:298MB)
2021-11-17 15:56:48,034 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_881_884_PeakCluster.serFS...
2021-11-17 15:56:48,035 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:48,120 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:48,443 INFO  [root] ==================================================================================
2021-11-17 15:56:48,443 INFO  [root] Processing DIA MS2 (mz range):878.0_881.0( 34/61 )
2021-11-17 15:56:48,472 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:48,472 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:48,831 INFO  [root] 74476 Peak curves found (Memory usage:290MB)
2021-11-17 15:56:48,833 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:48,833 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:49,230 INFO  [root] No of ion clusters:8 (Memory usage:296MB)
2021-11-17 15:56:49,230 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_878_881_PeakCluster.serFS...
2021-11-17 15:56:49,231 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:49,311 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:49,633 INFO  [root] ==================================================================================
2021-11-17 15:56:49,633 INFO  [root] Processing DIA MS2 (mz range):875.0_878.0( 35/61 )
2021-11-17 15:56:49,660 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:49,660 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:50,040 INFO  [root] 77271 Peak curves found (Memory usage:291MB)
2021-11-17 15:56:50,042 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:50,042 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:50,436 INFO  [root] No of ion clusters:6 (Memory usage:297MB)
2021-11-17 15:56:50,436 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_875_878_PeakCluster.serFS...
2021-11-17 15:56:50,437 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:50,524 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:50,858 INFO  [root] ==================================================================================
2021-11-17 15:56:50,858 INFO  [root] Processing DIA MS2 (mz range):872.0_875.0( 36/61 )
2021-11-17 15:56:50,892 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:50,892 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:51,341 INFO  [root] 80881 Peak curves found (Memory usage:294MB)
2021-11-17 15:56:51,343 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:51,343 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:51,783 INFO  [root] No of ion clusters:9 (Memory usage:300MB)
2021-11-17 15:56:51,783 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_872_875_PeakCluster.serFS...
2021-11-17 15:56:51,784 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:51,908 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:52,208 INFO  [root] ==================================================================================
2021-11-17 15:56:52,208 INFO  [root] Processing DIA MS2 (mz range):869.0_872.0( 37/61 )
2021-11-17 15:56:52,239 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:52,239 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:52,646 INFO  [root] 80006 Peak curves found (Memory usage:293MB)
2021-11-17 15:56:52,647 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:52,647 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:53,041 INFO  [root] No of ion clusters:10 (Memory usage:299MB)
2021-11-17 15:56:53,041 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_869_872_PeakCluster.serFS...
2021-11-17 15:56:53,042 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:53,135 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:53,459 INFO  [root] ==================================================================================
2021-11-17 15:56:53,460 INFO  [root] Processing DIA MS2 (mz range):866.0_869.0( 38/61 )
2021-11-17 15:56:53,488 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:53,488 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:53,877 INFO  [root] 80651 Peak curves found (Memory usage:294MB)
2021-11-17 15:56:53,878 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:53,878 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:54,281 INFO  [root] No of ion clusters:12 (Memory usage:300MB)
2021-11-17 15:56:54,281 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_866_869_PeakCluster.serFS...
2021-11-17 15:56:54,282 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:54,366 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:54,659 INFO  [root] ==================================================================================
2021-11-17 15:56:54,660 INFO  [root] Processing DIA MS2 (mz range):863.0_866.0( 39/61 )
2021-11-17 15:56:54,690 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:54,690 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:55,090 INFO  [root] 82590 Peak curves found (Memory usage:295MB)
2021-11-17 15:56:55,092 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:55,092 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:55,496 INFO  [root] No of ion clusters:12 (Memory usage:302MB)
2021-11-17 15:56:55,497 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_863_866_PeakCluster.serFS...
2021-11-17 15:56:55,497 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:55,621 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:55,945 INFO  [root] ==================================================================================
2021-11-17 15:56:55,945 INFO  [root] Processing DIA MS2 (mz range):860.0_863.0( 40/61 )
2021-11-17 15:56:55,977 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:55,977 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:56,409 INFO  [root] 97563 Peak curves found (Memory usage:301MB)
2021-11-17 15:56:56,411 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:56,411 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:56,849 INFO  [root] No of ion clusters:14 (Memory usage:309MB)
2021-11-17 15:56:56,849 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_860_863_PeakCluster.serFS...
2021-11-17 15:56:56,850 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:56,967 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:57,284 INFO  [root] ==================================================================================
2021-11-17 15:56:57,284 INFO  [root] Processing DIA MS2 (mz range):857.0_860.0( 41/61 )
2021-11-17 15:56:57,316 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:57,317 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:57,830 INFO  [root] 103122 Peak curves found (Memory usage:304MB)
2021-11-17 15:56:57,831 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:57,831 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:58,273 INFO  [root] No of ion clusters:12 (Memory usage:312MB)
2021-11-17 15:56:58,273 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_857_860_PeakCluster.serFS...
2021-11-17 15:56:58,273 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:58,407 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:56:58,719 INFO  [root] ==================================================================================
2021-11-17 15:56:58,719 INFO  [root] Processing DIA MS2 (mz range):854.0_857.0( 42/61 )
2021-11-17 15:56:58,754 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:56:58,754 INFO  [root] Smoothing detected signals......
2021-11-17 15:56:59,250 INFO  [root] 106710 Peak curves found (Memory usage:306MB)
2021-11-17 15:56:59,252 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:56:59,252 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:56:59,695 INFO  [root] No of ion clusters:18 (Memory usage:314MB)
2021-11-17 15:56:59,695 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_854_857_PeakCluster.serFS...
2021-11-17 15:56:59,696 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:56:59,856 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:00,210 INFO  [root] ==================================================================================
2021-11-17 15:57:00,210 INFO  [root] Processing DIA MS2 (mz range):851.0_854.0( 43/61 )
2021-11-17 15:57:00,251 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:00,251 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:00,777 INFO  [root] 105975 Peak curves found (Memory usage:306MB)
2021-11-17 15:57:00,778 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:00,778 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:01,224 INFO  [root] No of ion clusters:11 (Memory usage:314MB)
2021-11-17 15:57:01,224 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_851_854_PeakCluster.serFS...
2021-11-17 15:57:01,225 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:01,376 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:01,700 INFO  [root] ==================================================================================
2021-11-17 15:57:01,700 INFO  [root] Processing DIA MS2 (mz range):848.0_851.0( 44/61 )
2021-11-17 15:57:01,735 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:01,736 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:02,206 INFO  [root] 101215 Peak curves found (Memory usage:305MB)
2021-11-17 15:57:02,208 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:02,208 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:02,664 INFO  [root] No of ion clusters:7 (Memory usage:312MB)
2021-11-17 15:57:02,664 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_848_851_PeakCluster.serFS...
2021-11-17 15:57:02,665 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:02,786 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:03,110 INFO  [root] ==================================================================================
2021-11-17 15:57:03,110 INFO  [root] Processing DIA MS2 (mz range):845.0_848.0( 45/61 )
2021-11-17 15:57:03,143 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:03,143 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:03,614 INFO  [root] 97810 Peak curves found (Memory usage:303MB)
2021-11-17 15:57:03,616 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:03,616 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:04,052 INFO  [root] No of ion clusters:16 (Memory usage:310MB)
2021-11-17 15:57:04,052 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_845_848_PeakCluster.serFS...
2021-11-17 15:57:04,053 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:04,211 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:04,536 INFO  [root] ==================================================================================
2021-11-17 15:57:04,536 INFO  [root] Processing DIA MS2 (mz range):842.0_845.0( 46/61 )
2021-11-17 15:57:04,568 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:04,568 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:05,003 INFO  [root] 90891 Peak curves found (Memory usage:301MB)
2021-11-17 15:57:05,005 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:05,005 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:05,422 INFO  [root] No of ion clusters:12 (Memory usage:307MB)
2021-11-17 15:57:05,422 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_842_845_PeakCluster.serFS...
2021-11-17 15:57:05,423 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:05,548 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:05,878 INFO  [root] ==================================================================================
2021-11-17 15:57:05,878 INFO  [root] Processing DIA MS2 (mz range):839.0_842.0( 47/61 )
2021-11-17 15:57:05,907 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:05,907 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:06,334 INFO  [root] 90526 Peak curves found (Memory usage:301MB)
2021-11-17 15:57:06,336 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:06,336 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:06,755 INFO  [root] No of ion clusters:7 (Memory usage:308MB)
2021-11-17 15:57:06,755 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_839_842_PeakCluster.serFS...
2021-11-17 15:57:06,756 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:06,881 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:07,196 INFO  [root] ==================================================================================
2021-11-17 15:57:07,196 INFO  [root] Processing DIA MS2 (mz range):836.0_839.0( 48/61 )
2021-11-17 15:57:07,235 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:07,235 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:07,742 INFO  [root] 102423 Peak curves found (Memory usage:306MB)
2021-11-17 15:57:07,744 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:07,744 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:08,216 INFO  [root] No of ion clusters:12 (Memory usage:313MB)
2021-11-17 15:57:08,216 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_836_839_PeakCluster.serFS...
2021-11-17 15:57:08,217 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:08,371 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:08,690 INFO  [root] ==================================================================================
2021-11-17 15:57:08,690 INFO  [root] Processing DIA MS2 (mz range):833.0_836.0( 49/61 )
2021-11-17 15:57:08,725 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:08,725 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:09,239 INFO  [root] 112952 Peak curves found (Memory usage:310MB)
2021-11-17 15:57:09,241 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:09,241 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:09,732 INFO  [root] No of ion clusters:10 (Memory usage:318MB)
2021-11-17 15:57:09,732 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_833_836_PeakCluster.serFS...
2021-11-17 15:57:09,733 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:09,901 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:10,227 INFO  [root] ==================================================================================
2021-11-17 15:57:10,227 INFO  [root] Processing DIA MS2 (mz range):830.0_833.0( 50/61 )
2021-11-17 15:57:10,271 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:10,271 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:10,896 INFO  [root] 127718 Peak curves found (Memory usage:316MB)
2021-11-17 15:57:10,898 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:10,899 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:11,378 INFO  [root] No of ion clusters:7 (Memory usage:326MB)
2021-11-17 15:57:11,378 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_830_833_PeakCluster.serFS...
2021-11-17 15:57:11,379 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:11,541 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:11,861 INFO  [root] ==================================================================================
2021-11-17 15:57:11,861 INFO  [root] Processing DIA MS2 (mz range):827.0_830.0( 51/61 )
2021-11-17 15:57:11,903 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:11,903 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:12,510 INFO  [root] 139090 Peak curves found (Memory usage:320MB)
2021-11-17 15:57:12,511 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:12,511 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:13,022 INFO  [root] No of ion clusters:7 (Memory usage:331MB)
2021-11-17 15:57:13,022 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_827_830_PeakCluster.serFS...
2021-11-17 15:57:13,023 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:13,197 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:13,511 INFO  [root] ==================================================================================
2021-11-17 15:57:13,511 INFO  [root] Processing DIA MS2 (mz range):824.0_827.0( 52/61 )
2021-11-17 15:57:13,555 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:13,555 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:14,197 INFO  [root] 142668 Peak curves found (Memory usage:323MB)
2021-11-17 15:57:14,199 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:14,199 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:14,728 INFO  [root] No of ion clusters:9 (Memory usage:333MB)
2021-11-17 15:57:14,728 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_824_827_PeakCluster.serFS...
2021-11-17 15:57:14,729 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:14,947 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:15,257 INFO  [root] ==================================================================================
2021-11-17 15:57:15,257 INFO  [root] Processing DIA MS2 (mz range):821.0_824.0( 53/61 )
2021-11-17 15:57:15,311 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:15,311 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:16,045 INFO  [root] 161321 Peak curves found (Memory usage:330MB)
2021-11-17 15:57:16,046 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:16,047 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:16,612 INFO  [root] No of ion clusters:9 (Memory usage:342MB)
2021-11-17 15:57:16,612 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_821_824_PeakCluster.serFS...
2021-11-17 15:57:16,613 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:16,865 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:17,214 INFO  [root] ==================================================================================
2021-11-17 15:57:17,214 INFO  [root] Processing DIA MS2 (mz range):818.0_821.0( 54/61 )
2021-11-17 15:57:17,267 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:17,267 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:17,960 INFO  [root] 157465 Peak curves found (Memory usage:329MB)
2021-11-17 15:57:17,962 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:17,962 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:18,477 INFO  [root] No of ion clusters:8 (Memory usage:341MB)
2021-11-17 15:57:18,477 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_818_821_PeakCluster.serFS...
2021-11-17 15:57:18,478 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:18,692 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:19,014 INFO  [root] ==================================================================================
2021-11-17 15:57:19,014 INFO  [root] Processing DIA MS2 (mz range):815.0_818.0( 55/61 )
2021-11-17 15:57:19,059 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:19,059 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:19,715 INFO  [root] 152935 Peak curves found (Memory usage:326MB)
2021-11-17 15:57:19,716 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:19,716 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:20,241 INFO  [root] No of ion clusters:7 (Memory usage:338MB)
2021-11-17 15:57:20,241 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_815_818_PeakCluster.serFS...
2021-11-17 15:57:20,242 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:20,462 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:20,785 INFO  [root] ==================================================================================
2021-11-17 15:57:20,785 INFO  [root] Processing DIA MS2 (mz range):812.0_815.0( 56/61 )
2021-11-17 15:57:20,831 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:20,831 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:21,622 INFO  [root] 136506 Peak curves found (Memory usage:321MB)
2021-11-17 15:57:21,624 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:21,624 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:22,136 INFO  [root] No of ion clusters:7 (Memory usage:331MB)
2021-11-17 15:57:22,136 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_812_815_PeakCluster.serFS...
2021-11-17 15:57:22,137 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:22,373 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:22,703 INFO  [root] ==================================================================================
2021-11-17 15:57:22,703 INFO  [root] Processing DIA MS2 (mz range):809.0_812.0( 57/61 )
2021-11-17 15:57:22,744 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:22,744 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:23,324 INFO  [root] 130719 Peak curves found (Memory usage:318MB)
2021-11-17 15:57:23,326 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:23,326 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:23,835 INFO  [root] No of ion clusters:13 (Memory usage:327MB)
2021-11-17 15:57:23,835 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_809_812_PeakCluster.serFS...
2021-11-17 15:57:23,835 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:24,034 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:24,359 INFO  [root] ==================================================================================
2021-11-17 15:57:24,359 INFO  [root] Processing DIA MS2 (mz range):806.0_809.0( 58/61 )
2021-11-17 15:57:24,406 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:24,407 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:25,012 INFO  [root] 129265 Peak curves found (Memory usage:317MB)
2021-11-17 15:57:25,014 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:25,014 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:25,505 INFO  [root] No of ion clusters:5 (Memory usage:327MB)
2021-11-17 15:57:25,505 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_806_809_PeakCluster.serFS...
2021-11-17 15:57:25,505 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:25,741 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:26,063 INFO  [root] ==================================================================================
2021-11-17 15:57:26,063 INFO  [root] Processing DIA MS2 (mz range):803.0_806.0( 59/61 )
2021-11-17 15:57:26,104 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:26,104 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:26,738 INFO  [root] 130500 Peak curves found (Memory usage:318MB)
2021-11-17 15:57:26,739 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:26,739 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:27,228 INFO  [root] No of ion clusters:6 (Memory usage:328MB)
2021-11-17 15:57:27,228 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_803_806_PeakCluster.serFS...
2021-11-17 15:57:27,229 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:27,468 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:27,784 INFO  [root] ==================================================================================
2021-11-17 15:57:27,784 INFO  [root] Processing DIA MS2 (mz range):800.0_803.0( 60/61 )
2021-11-17 15:57:27,815 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:27,815 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:28,277 INFO  [root] 67259 Peak curves found (Memory usage:294MB)
2021-11-17 15:57:28,279 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:28,279 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:28,653 INFO  [root] No of ion clusters:7 (Memory usage:299MB)
2021-11-17 15:57:28,653 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_800_803_PeakCluster.serFS...
2021-11-17 15:57:28,654 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:28,787 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:29,121 INFO  [root] ==================================================================================
2021-11-17 15:57:29,121 INFO  [root] Processing DIA MS2 (mz range):797.0_800.0( 61/61 )
2021-11-17 15:57:29,141 INFO  [root] Processing all scans to detect possible m/z peak curves and
2021-11-17 15:57:29,141 INFO  [root] Smoothing detected signals......
2021-11-17 15:57:29,951 INFO  [root] 63741 Peak curves found (Memory usage:297MB)
2021-11-17 15:57:29,952 INFO  [root] Grouping isotopic peak curves........
2021-11-17 15:57:29,952 INFO  [root] Building PeakCurve Mass-RT KD tree
2021-11-17 15:57:30,333 INFO  [root] No of ion clusters:50 (Memory usage:302MB)
2021-11-17 15:57:30,333 INFO  [root] Writing PeakCluster serialization to file:JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_797_800_PeakCluster.serFS...
2021-11-17 15:57:30,334 INFO  [root] Building precursor-fragment pairs for MS1 features....
2021-11-17 15:57:30,721 INFO  [root] Building precursor-fragment pairs for unfragmented ions....
2021-11-17 15:57:31,204 INFO  [root] ==================================================================================
2021-11-17 15:57:32,222 INFO  [root] C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.mzXML processed time:0 hour, 1 min, 57 sec
2021-11-17 15:57:32,222 INFO  [root] Job complete
2021-11-17 15:57:32,222 INFO  [root] =================================================================================================
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\diaumpire_se.log C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\diaumpire_se.log
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Peak C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.DIAWindowsFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.RTidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q1 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q2 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q3 C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanidxFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanPosFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanRTFS C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_diasetting.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_params.ser C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mgf C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar;/C:/Users/jossmith/MSFragger/FragPipe-17.1/fragpipe/lib/commons-io-2.6.jar com.github.chhh.utils.FileMove --no-err C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Peak
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.DIAWindowsFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.RTidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q1
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q2
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanClusterMapping_Q3
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanidxFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanPosFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA.ScanRTFS
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_diasetting.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_params.ser
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mgf
Process 'UmpireSe' finished, exit code: 0
UmpireSe
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib\fragpipe-17.1.jar com.github.chhh.utils.FileDelete C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mgf
Process 'UmpireSe' finished, exit code: 0
MSFragger [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
java -jar -Dfile.encoding=UTF-8 -Xmx25G C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\MSFragger-3.4.jar C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\fragger_dda.params C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML
MSFragger version MSFragger-3.4
Batmass-IO version 1.23.6
timsdata library version timsdata-2-8-7-1
(c) University of Michigan
RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved.
System OS: Windows 10, Architecture: AMD64
Java Info: 1.8.0_152, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation
JVM started with 22 GB memory
data_type = 0 and output_report_topN > 1. Change output_report_topN to 1.
Checking database...
Checking spectral files...
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML: Scans = 238
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML: Scans = 645
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML: Scans = 1577
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML: Scans = 2275
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML: Scans = 4762
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML: Scans = 4477
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML: Scans = 550
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML: Scans = 2980
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML: Scans = 1960
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML: Scans = 257
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML: Scans = 3596
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML: Scans = 490
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML: Scans = 3099
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML: Scans = 5610
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML: Scans = 4362
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML: Scans = 602
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML: Scans = 7157
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML: Scans = 4635
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML: Scans = 1245
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML: Scans = 12732
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML: Scans = 3071
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML: Scans = 1296
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML: Scans = 1751
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML: Scans = 10987
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML: Scans = 1994
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML: Scans = 1174
C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML: Scans = 6871
precursor_mass_mode = CORRECTED does not support specified spectral files. Using SELECTED instead.
***********************************FIRST SEARCH************************************
Parameters:
num_threads = 7
database_name = C:\Users\jossmith\MSFragger\Philosopher\2020-02-03-decoys-reviewed-contam-UP000005640.fas
decoy_prefix = rev_
precursor_mass_lower = -10.0
precursor_mass_upper = 10.0
precursor_mass_units = 1
data_type = 0
precursor_true_tolerance = 10.0
precursor_true_units = 1
fragment_mass_tolerance = 10.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = false
write_calibrated_mgf = 1
isotope_error = 0/1
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = all
precursor_mass_mode = SELECTED
localize_delta_mass = false
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = trypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = P
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = tsv_pepxml
output_report_topN = 1
output_max_expect = 10.0
report_alternative_proteins = false
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 5
digest_max_length = 30
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
deisotope = 1
deneutralloss = true
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 100
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.01
intensity_transform = 0
remove_precursor_peak = 0
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = true
variable_mod_01 = 15.994900 M 3
variable_mod_02 = 42.010600 [^ 1
variable_mod_06 = 57.021460 Cys Carbamidomethylation 2
add_A_alanine = 0.000000
add_B_user_amino_acid = 0.000000
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.000000
add_E_glutamic_acid = 0.000000
add_F_phenylalanine = 0.000000
add_G_glycine = 0.000000
add_H_histidine = 0.000000
add_I_isoleucine = 0.000000
add_J_user_amino_acid = 0.000000
add_K_lysine = 0.000000
add_L_leucine = 0.000000
add_M_methionine = 0.000000
add_N_asparagine = 0.000000
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.000000  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.000000
add_Q_glutamine = 0.000000
add_R_arginine = 0.000000
add_S_serine = 0.000000
add_T_threonine = 0.000000
add_U_user_amino_acid = 0.000000  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.000000
add_W_tryptophan = 0.000000
add_X_user_amino_acid = 0.000000
add_Y_tyrosine = 0.000000
add_Z_user_amino_acid = 0.000000
Number of unique peptides
	of length 5: 135928
	of length 6: 244642
	of length 7: 262386
	of length 8: 253508
	of length 9: 251156
	of length 10: 238909
	of length 11: 227500
	of length 12: 217674
	of length 13: 213363
	of length 14: 198642
	of length 15: 190674
	of length 16: 178517
	of length 17: 168036
	of length 18: 162391
	of length 19: 157937
	of length 20: 144010
	of length 21: 137906
	of length 22: 129710
	of length 23: 121616
	of length 24: 116620
	of length 25: 109512
	of length 26: 102411
	of length 27: 97724
	of length 28: 95933
	of length 29: 85853
	of length 30: 81439
In total 4323997 peptides.
Generated 9153102 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.05 Da.
305513116 fragments to be searched in 1 slices (4.55 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 7.71 s
	001. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML 0.3 s | deisotoping 0.3 s
		[progress: 1563/1563 (100%) - 5622 spectra/s] 0.3s | postprocessing 0.0 s
	002. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 1935/1935 (100%) - 16974 spectra/s] 0.1s | postprocessing 0.0 s
	003. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 257/257 (100%) - 2402 spectra/s] 0.1s | postprocessing 0.0 s
	004. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML 0.1 s | deisotoping 0.1 s
		[progress: 4468/4468 (100%) - 13377 spectra/s] 0.3s | postprocessing 0.0 s
	005. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML 0.2 s | deisotoping 0.1 s
		[progress: 7115/7115 (100%) - 15603 spectra/s] 0.5s | postprocessing 0.0 s
	006. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML 0.1 s | deisotoping 0.0 s
		[progress: 1245/1245 (100%) - 5321 spectra/s] 0.2s | postprocessing 0.0 s
	007. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML 0.1 s | deisotoping 0.0 s
		[progress: 3057/3057 (100%) - 14285 spectra/s] 0.2s | postprocessing 0.0 s
	008. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 4741/4741 (100%) - 19194 spectra/s] 0.2s | postprocessing 0.0 s
	009. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 550/550 (100%) - 5140 spectra/s] 0.1s | postprocessing 0.0 s
	010. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML 0.1 s | deisotoping 0.1 s
		[progress: 3094/3094 (100%) - 13000 spectra/s] 0.2s | postprocessing 0.0 s
	011. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 4624/4624 (100%) - 13481 spectra/s] 0.3s | postprocessing 0.0 s
	012. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 645/645 (100%) - 5864 spectra/s] 0.1s | postprocessing 0.0 s
	013. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML 0.1 s | deisotoping 0.0 s
		[progress: 2973/2973 (100%) - 13893 spectra/s] 0.2s | postprocessing 0.0 s
	014. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 4344/4344 (100%) - 17516 spectra/s] 0.2s | postprocessing 0.0 s
	015. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 600/600 (100%) - 5217 spectra/s] 0.1s | postprocessing 0.0 s
	016. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML 0.2 s | deisotoping 0.1 s
		[progress: 5604/5604 (100%) - 12398 spectra/s] 0.5s | postprocessing 0.0 s
	017. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML 0.4 s | deisotoping 0.1 s
		[progress: 10973/10973 (100%) - 18018 spectra/s] 0.6s | postprocessing 0.0 s
	018. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 1172/1172 (100%) - 5376 spectra/s] 0.2s | postprocessing 0.0 s
	019. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML 0.3 s | deisotoping 0.2 s
		[progress: 6869/6869 (100%) - 19910 spectra/s] 0.3s | postprocessing 0.0 s
	020. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML 0.3 s | deisotoping 0.1 s
		[progress: 12730/12730 (100%) - 28226 spectra/s] 0.5s | postprocessing 0.0 s
	021. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 1296/1296 (100%) - 11469 spectra/s] 0.1s | postprocessing 0.0 s
	022. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML 0.0 s | deisotoping 0.0 s
		[progress: 1737/1737 (100%) - 15509 spectra/s] 0.1s | postprocessing 0.0 s
	023. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML 0.0 s | deisotoping 0.0 s
		[progress: 1967/1967 (100%) - 18383 spectra/s] 0.1s | postprocessing 0.0 s
	024. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 236/236 (100%) - 2052 spectra/s] 0.1s | postprocessing 0.0 s
	025. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML 0.1 s | deisotoping 0.0 s
		[progress: 2263/2263 (100%) - 22406 spectra/s] 0.1s | postprocessing 0.0 s
	026. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 3546/3546 (100%) - 34427 spectra/s] 0.1s | postprocessing 0.0 s
	027. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 487/487 (100%) - 4822 spectra/s] 0.1s | postprocessing 0.0 s
***************************FIRST SEARCH DONE IN 0.481 MIN**************************

*********************MASS CALIBRATION AND PARAMETER OPTIMIZATION*******************
-----|---------------|---------------|---------------|---------------
     |  MS1   (Old)  |  MS1   (New)  |  MS2   (Old)  |  MS2   (New)  
-----|---------------|---------------|---------------|---------------
 Run |  Median  MAD  |  Median  MAD  |  Median  MAD  |  Median  MAD  
 001 |  -1.26   1.35 |  -0.19   1.35 |  -4.65   1.52 |  -0.20   1.39  
 002 | Not enough data to perform mass calibration. Using the uncalibrated data.
 003 | Not enough data to perform mass calibration. Using the uncalibrated data.
 004 |  -0.46   1.44 |  -0.01   1.44 |  -3.14   1.95 |  -0.54   1.79  
 005 | Not enough data to perform mass calibration. Using the uncalibrated data.
 006 | Not enough data to perform mass calibration. Using the uncalibrated data.
 007 |  -0.80   1.57 |  -0.19   1.57 |  -4.08   1.65 |  -0.36   1.39  
 008 | Not enough data to perform mass calibration. Using the uncalibrated data.
 009 | Not enough data to perform mass calibration. Using the uncalibrated data.
 010 |  -0.91   1.37 |  -0.09   1.61 |  -3.75   1.66 |  -0.56   1.39  
 011 | Not enough data to perform mass calibration. Using the uncalibrated data.
 012 | Not enough data to perform mass calibration. Using the uncalibrated data.
 013 |  -0.64   1.37 |  -0.11   1.37 |  -3.97   1.70 |  -0.60   1.53  
 014 | Not enough data to perform mass calibration. Using the uncalibrated data.
 015 | Not enough data to perform mass calibration. Using the uncalibrated data.
 016 |  -0.83   1.35 |  -0.02   1.38 |  -2.91   1.80 |  -0.08   1.53  
 017 | Not enough data to perform mass calibration. Using the uncalibrated data.
 018 | Not enough data to perform mass calibration. Using the uncalibrated data.
 019 |  -0.74   1.41 |   0.19   1.41 |  -2.07   1.91 |  -0.10   1.63  
 020 | Not enough data to perform mass calibration. Using the uncalibrated data.
 021 | Not enough data to perform mass calibration. Using the uncalibrated data.
 022 |  -0.96   1.38 |  -0.35   1.38 |  -4.39   1.46 |  -0.72   1.18  
 023 | Not enough data to perform mass calibration. Using the uncalibrated data.
 024 | Not enough data to perform mass calibration. Using the uncalibrated data.
 025 |  -0.74   1.20 |  -0.33   1.20 |  -3.88   1.48 |  -0.57   1.32  
 026 | Not enough data to perform mass calibration. Using the uncalibrated data.
 027 | Not enough data to perform mass calibration. Using the uncalibrated data.
-----|---------------|---------------|---------------|---------------
Finding the optimal parameters:
-------|-------|-------|-------|-------|-------|-------|-------|-------
  MS2  |    5  |    7  |   10  |   15  |   20  |   25  |   30  |   50  
-------|-------|-------|-------|-------|-------|-------|-------|-------
 Count |   1316|   1335|   1315| skip rest
-------|-------|-------|-------|-------|-------|-------|-------|-------
-------|-------|-------|-------|-------|-------|-------
 Peaks | 300_0 | 200_0 | 175_0 | 150_1 | 125_1 | 100_1 
-------|-------|-------|-------|-------|-------|-------
 Count |   1415|   1392| skip rest
-------|-------|-------|-------|-------|-------|-------
-------|-------
 Int.  |    1  
-------|-------
 Count |   1414
-------|-------
-------|-------
 Rm P. |    1  
-------|-------
 Count |   1421
-------|-------
New fragment_mass_tolerance = 7 PPM
New use_topN_peaks = 300
New minimum_ratio = 0.000000
New intensity_transform = 0
New remove_precursor_peak = 1
************MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 1.084 MIN*********

************************************MAIN SEARCH************************************
data_type = 0 and output_report_topN > 1. Change output_report_topN to 1.
Checking database...
Parameters:
num_threads = 7
database_name = C:\Users\jossmith\MSFragger\Philosopher\2020-02-03-decoys-reviewed-contam-UP000005640.fas
decoy_prefix = rev_
precursor_mass_lower = -150.0
precursor_mass_upper = 500.0
precursor_mass_units = 0
data_type = 0
precursor_true_tolerance = 10.0
precursor_true_units = 1
fragment_mass_tolerance = 7.0
fragment_mass_units = 1
calibrate_mass = 2
use_all_mods_in_first_search = false
write_calibrated_mgf = 1
isotope_error = 0
mass_offsets = 0
labile_search_mode = OFF
restrict_deltamass_to = CHKYWST
precursor_mass_mode = SELECTED
localize_delta_mass = true
delta_mass_exclude_ranges = (-1.5,3.5)
fragment_ion_series = b,y
ion_series_definitions = 
search_enzyme_name = trypsin
search_enzyme_sense_1 = C
search_enzyme_cut_1 = KR
search_enzyme_nocut_1 = P
allowed_missed_cleavage_1 = 2
num_enzyme_termini = 2
clip_nTerm_M = true
allow_multiple_variable_mods_on_residue = false
max_variable_mods_per_peptide = 3
max_variable_mods_combinations = 5000
output_format = tsv_pepxml
output_report_topN = 1
output_max_expect = 10.0
report_alternative_proteins = true
override_charge = false
precursor_charge_low = 1
precursor_charge_high = 4
digest_min_length = 5
digest_max_length = 30
digest_mass_range_low = 500.0
digest_mass_range_high = 5000.0
max_fragment_charge = 2
deisotope = 1
deneutralloss = true
track_zero_topN = 0
zero_bin_accept_expect = 0.0
zero_bin_mult_expect = 1.0
add_topN_complementary = 0
minimum_peaks = 15
use_topN_peaks = 300
minIonsScoring = 2
min_matched_fragments = 4
minimum_ratio = 0.0
intensity_transform = 0
remove_precursor_peak = 1
remove_precursor_range = -1.500000,1.500000
clear_mz_range_low = 0.0
clear_mz_range_high = 0.0
excluded_scan_list_file = 
mass_diff_to_variable_mod = 0
min_sequence_matches = 2
check_spectral_files = true
variable_mod_01 = 15.994900 M 3
variable_mod_02 = 42.010600 [^ 1
variable_mod_06 = 57.021460 Cys Carbamidomethylation 2
add_A_alanine = 0.000000
add_B_user_amino_acid = 0.000000
add_Cterm_peptide = 0.0
add_Cterm_protein = 0.0
add_D_aspartic_acid = 0.000000
add_E_glutamic_acid = 0.000000
add_F_phenylalanine = 0.000000
add_G_glycine = 0.000000
add_H_histidine = 0.000000
add_I_isoleucine = 0.000000
add_J_user_amino_acid = 0.000000
add_K_lysine = 0.000000
add_L_leucine = 0.000000
add_M_methionine = 0.000000
add_N_asparagine = 0.000000
add_Nterm_peptide = 0.0
add_Nterm_protein = 0.0
add_O_user_amino_acid = 0.000000  # O = pyrrolysine (237.14773 Da)
add_P_proline = 0.000000
add_Q_glutamine = 0.000000
add_R_arginine = 0.000000
add_S_serine = 0.000000
add_T_threonine = 0.000000
add_U_user_amino_acid = 0.000000  # U = selenocysteine (150.95363 Da)
add_V_valine = 0.000000
add_W_tryptophan = 0.000000
add_X_user_amino_acid = 0.000000
add_Y_tyrosine = 0.000000
add_Z_user_amino_acid = 0.000000
Number of unique peptides
	of length 5: 135928
	of length 6: 244642
	of length 7: 262386
	of length 8: 253508
	of length 9: 251156
	of length 10: 238909
	of length 11: 227500
	of length 12: 217674
	of length 13: 213363
	of length 14: 198642
	of length 15: 190674
	of length 16: 178517
	of length 17: 168036
	of length 18: 162391
	of length 19: 157937
	of length 20: 144010
	of length 21: 137906
	of length 22: 129710
	of length 23: 121616
	of length 24: 116620
	of length 25: 109512
	of length 26: 102411
	of length 27: 97724
	of length 28: 95933
	of length 29: 85853
	of length 30: 81439
In total 4323997 peptides.
Generated 9153102 modified peptides.
Number of peptides with more than 5000 modification patterns: 0
Selected fragment index width 0.01 Da.
611026232 fragments to be searched in 1 slices (9.11 GB total)
Operating on slice 1 of 1: 
	Fragment index slice generated in 21.92 s
	001. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzBIN_calibrated 0.0 s
		[progress: 1510/1510 (100%) - 40 spectra/s] 37.8s | postprocessing 0.5 s
	002. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 1935/1935 (100%) - 94 spectra/s] 20.7s | postprocessing 0.3 s
	003. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 257/257 (100%) - 34 spectra/s] 7.6s | postprocessing 0.1 s
	004. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzBIN_calibrated 0.1 s
		[progress: 4409/4409 (100%) - 33 spectra/s] 135.3s | postprocessing 0.5 s
	005. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML 0.2 s | deisotoping 0.1 s
		[progress: 7115/7115 (100%) - 60 spectra/s] 118.1s | postprocessing 0.7 s
	006. JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 1245/1245 (100%) - 26 spectra/s] 47.9s | postprocessing 0.2 s
	007. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzBIN_calibrated 0.0 s
		[progress: 2996/2996 (100%) - 48 spectra/s] 62.0s | postprocessing 0.3 s
	008. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 4741/4741 (100%) - 86 spectra/s] 55.3s | postprocessing 0.4 s
	009. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 550/550 (100%) - 37 spectra/s] 14.8s | postprocessing 0.1 s
	010. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzBIN_calibrated 0.0 s
		[progress: 3049/3049 (100%) - 34 spectra/s] 88.4s | postprocessing 0.4 s
	011. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 4624/4624 (100%) - 66 spectra/s] 70.4s | postprocessing 0.4 s
	012. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 645/645 (100%) - 26 spectra/s] 24.6s | postprocessing 0.1 s
	013. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzBIN_calibrated 0.0 s
		[progress: 2913/2913 (100%) - 45 spectra/s] 64.7s | postprocessing 0.3 s
	014. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 4344/4344 (100%) - 76 spectra/s] 57.2s | postprocessing 0.4 s
	015. JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 600/600 (100%) - 32 spectra/s] 18.5s | postprocessing 0.1 s
	016. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzBIN_calibrated 0.1 s
		[progress: 5561/5561 (100%) - 31 spectra/s] 178.2s | postprocessing 0.6 s
	017. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML 0.3 s | deisotoping 0.1 s
		[progress: 10973/10973 (100%) - 58 spectra/s] 188.7s | postprocessing 1.2 s
	018. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 1172/1172 (100%) - 26 spectra/s] 44.3s | postprocessing 0.1 s
	019. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzBIN_calibrated 0.1 s
		[progress: 6815/6815 (100%) - 27 spectra/s] 253.4s | postprocessing 0.7 s
	020. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML 0.3 s | deisotoping 0.2 s
		[progress: 12730/12730 (100%) - 51 spectra/s] 251.3s | postprocessing 1.2 s
	021. JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML 0.1 s | deisotoping 0.0 s
		[progress: 1296/1296 (100%) - 22 spectra/s] 58.9s | postprocessing 0.1 s
	022. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzBIN_calibrated 0.0 s
		[progress: 1668/1668 (100%) - 60 spectra/s] 27.9s | postprocessing 0.2 s
	023. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML 0.0 s | deisotoping 0.0 s
		[progress: 1967/1967 (100%) - 107 spectra/s] 18.4s | postprocessing 0.2 s
	024. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 236/236 (100%) - 37 spectra/s] 6.4s | postprocessing 0.0 s
	025. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzBIN_calibrated 0.0 s
		[progress: 2205/2205 (100%) - 52 spectra/s] 42.2s | postprocessing 0.2 s
	026. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML 0.1 s | deisotoping 0.0 s
		[progress: 3546/3546 (100%) - 91 spectra/s] 39.0s | postprocessing 0.3 s
	027. JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML 0.0 s | deisotoping 0.0 s
		[progress: 487/487 (100%) - 39 spectra/s] 12.4s | postprocessing 0.1 s
***************************MAIN SEARCH DONE IN 33.210 MIN***************************

*******************************TOTAL TIME 34.775 MIN********************************
Process 'MSFragger' finished, exit code: 0
PeptideProphet [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev_ --database C:\Users\jossmith\MSFragger\Philosopher\2020-02-03-decoys-reviewed-contam-UP000005640.fas --combine JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.pepXML JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.pepXML
INFO[16:32:26] Executing PeptideProphet  v4.1.0             
 file 1: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.pepXML
 file 2: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.pepXML
 file 3: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.pepXML
 file 4: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.pepXML
 file 5: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.pepXML
 file 6: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.pepXML
 file 7: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.pepXML
 file 8: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.pepXML
 file 9: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.pepXML
 file 10: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.pepXML
 file 11: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.pepXML
 file 12: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.pepXML
 file 13: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.pepXML
 file 14: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.pepXML
 file 15: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.pepXML
 file 16: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.pepXML
 file 17: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.pepXML
 file 18: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.pepXML
 file 19: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.pepXML
 file 20: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.pepXML
 file 21: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.pepXML
 file 22: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.pepXML
 file 23: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.pepXML
 file 24: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.pepXML
 file 25: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.pepXML
 file 26: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.pepXML
 file 27: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.pepXML
 processed altogether 80643 results
INFO: Results written to file: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml

  - C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml
  - Building Commentz-Walter keyword tree...
  - Searching the tree...
  - Linking duplicate entries...
  - Printing results...

Using Decoy Label "rev_".
Decoy Probabilities will be reported.
Using non-parametric distributions
 (X! Tandem) (using Tandem's expectation score for modeling)
using search_offsets in mass mixture distr: 0
init with X! Tandem trypsin 
 PeptideProphet  (TPP v5.2.1-dev Flammagenitus, Build 201906281613-exported (Windows_NT-x86_64)) AKeller@ISB
 read in 25975 1+, 27652 2+, 15212 3+, 5894 4+, 2359 5+, 0 6+, and 0 7+ spectra.
Found 28498 Decoys, and 48594 Non-Decoys
MS Instrument info: Manufacturer: UNKNOWN, Model: UNKNOWN, Ionization: UNKNOWN, Analyzer: UNKNOWN, Detector: UNKNOWN

INFO: Processing standard MixtureModel ... 
Initialising statistical models ...
Iterations: .........10.........20.......
WARNING: Mixture model quality test failed for charge (1+).
WARNING: Mixture model quality test failed for charge (5+).
WARNING: Mixture model quality test failed for charge (6+).
WARNING: Mixture model quality test failed for charge (7+).
model complete after 28 iterations
INFO[16:34:36] Done                                         
Process 'PeptideProphet' finished, exit code: 0
Rewrite pepxml [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
java -cp C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\lib/* com.dmtavt.fragpipe.util.RewritePepxml C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML
Fixing pepxml: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml
Writing output to: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml335192274085892006.temp-rewrite
Deleting file: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml
Moving rewritten file to original location: [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml335192274085892006.temp-rewrite] -> [C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml]
Process 'Rewrite pepxml' finished, exit code: 0
ProteinProphet [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\filelist_proteinprophet.txt
INFO[16:34:47] Executing ProteinProphet  v4.1.0             
ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v6.0.0-rc15 Noctilucent, Build 202105101442-exported (Windows_NT-x86_64))
 (no FPKM) (using degen pep info)
Reading in C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml...
...read in 0 1+, 12623 2+, 8063 3+, 3193 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05

Initializing 9969 peptide weights: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating protein lengths and molecular weights from database c:/Users/jossmith/MSFragger/Philosopher/2020-02-03-decoys-reviewed-contam-UP000005640.fas
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........1000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........2000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........3000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........4000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........5000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........6000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........7000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........8000
.........:.........:.........:.........:.........:.........:.........WARNING: Found the following zero-mass residues in protein entry rev_sp|Q16881|TRXR1_HUMAN : U
GUCGAQLISAGSRKTVSLTTFVEACVPHIGITSDLQKKTLGCKLAAAFGQTVEGANPGLVHFGVVRENDKTNCIIKAYCKNNDRSPITWELPWFYSHYVEINEEGFKEVAKEESLGCAGYELPTFVTTPVNEYDCKVTSGAYLRQALLRGAQIAVPTLEVKDELIDGIAYIYPVNTQEEDTVPIKGTKENIKVGVTELGIKRTCADRGIALMVTNYEGEIIEESNTSQAVVRLRGPTGAEIQEVKIPVFQRIFKIGHEEMHEGIKNAMDQDFGRLLISRVMVTVDLGIGALFGACELAVYSAGVVLTKGPCYPLSFLDDSSICYEKDGPIGLYRPREGTAILFREASYIKEKGKNNTAKIRHPGIFQGYANEYVVKKERLAVRYGWNLSGIHNQVAEIMRDWDHKVTEEVKWGYNRSDQLAQGLLAAQHMLKKPICGVNVCTGGLGWRTGLPTPTVFDLVMVKKGYQAAEKAAALGGSGGGIIILDYDYSKPLDEPGNMKLLKQLRGEQYAKLTPGHGGIKRQKVFVVPLDTEAALESLTGELARGDETQDLELVFYPVCLSKFLKKVETCRTCTSRSFIVVSHGDIYAQLLARSDATATSTFGAPNEPLTKGPHHDKASRRRGDGNKGKTQLETPAAAAVAKGEACGM
:.........:.........:.........9000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........10000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........11000
.........:.........:.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q86VQ6|TRXR3_HUMAN : U
GUCGKQTIDLGSSKTIELTTFVEGCTPHIGITDDLLQKTLGCKMAAAFGQTVEGANPGLIHFGIVRDHDFKNCIIKAYCTNNERGAVTWELPWFLTHYIELNEKKYVEIAKEESLGCCGYELPTFVTTPVNIYDCKELSAGFLRQALLKGSQIAVPTLEPKDELIDGVAYVYPVNTQEVDNVPIKGSKENIKVGIKELGIKRTCSDRGIALLVTNYVGEITETGETSKALVKLKGPSGKELQQVMVPIFKRLFKVGHQEMYSGVKEAMEQDFGRLLISRVMVTVDLGFGALFGACELAVYSAGVVLTKGPCYPLSFLDDSTICYEKDGQIGLYRPREGTAIVFQAATYYTEQGKKNTAKIKHHEVFEGYSNVYAVAKERLSLRYGWNLSSIHNQIAKTMTEWNHRVQQNYEWGFKRSDCLAQGLLAAQHMLKKPICGVNVCTGGLGWSTGQPSPVVFDLVMVKKGLIAAEKACSLGGSGGGIIILDYDYALDEQLLKQLLGSQYAQFTQDCGGVHVKNVFINPVTKQNTIESLVEQVRAGDDVQDLELVNCEVGLSSFLEKVRTSHPCYSKSFIVVRSREILGVLHRRLEERAESSRSPGPSSLRARRGPPSLVRAGRVHGSRRNPADGAKGPGPSQPPSREM
..:.........:.........12000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........13000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........14000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........15000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........16000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........17000
.........:.........:.........:.........:.........:.........:.........:.........:.......WARNING: Found the following zero-mass residues in protein entry rev_sp|Q9NNW7|TRXR2_HUMAN : U
GUCGTVTPDLGSRKSIRLKVVEESCTPHIGVTRMVQAYSAGCKIGLAFGQTVEGANPGLFHLGLVLQPPERLCVMKVYCQSADRGAVTFELPKYHAHYVEVHEQGHRAVAEEESLGVCGYELPTFVTTPVNDYDMLDSSGGFLRQVLLRGAMIAIPTLEPRGEVVDGIAYIHPVSTAERSDVLIKQTDPSTDVGAKELNLSRTDPVRGIAWLVTDFTGTDEKGTTSDEWTVQLQGDPLRRVRSPACGRLFRTGHSAMHEIVMSSMQQDFGRLPISRMMITTDLGIGTLFGACELAVYSAGVVLTKGPSEKLWFIDDSTIGYELAGEIHTPYRPRGGTAIIIHDASLLIEKGGKAVGCVTHEDVFSAKINFYKVKRDQLQVRHGWNLSKVHNQVAEAMKRWDHPVPQAVEWGYNPADQILGGLLAAQHMLKKPICGVNVCTGGLGWRTGQPSPEVYDVVAVKRGLQAAEKACALGGSGGGVVLLDYDRQGAAAGRAAGRVGGAVAQTRWRFRGGLGRLAVAMAAM
..:.........18000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........19000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........20000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........21000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........22000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........23000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.WARNING: Found the following zero-mass residues in protein entry sp|P07203|GPX1_HUMAN : U
MCAARLAAAAAAAQSVYAFSARPLAGGEPVSLGSLRGKVLLIENVASLUGTTVRDYTQMNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNGAGAHPLFAFLREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGVPLRRYSRRFQTIDIEPDIEALLSQGPSCA
........24000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........25000
.........:.........WARNING: Found the following zero-mass residues in protein entry sp|P22352|GPX3_HUMAN : U
MARLLQASCLLSLLLAGFVSQSRGQEKSKMDCHGGISGTIYEYGALTIDGEEYIPFKQYAGKYVLFVNVASYUGLTGQYIELNALQEELAPFGLVILGFPCNQFGKQEPGENSEILPTLKYVRPGGGFVPNFQLFEKGDVNGEKEQKFYTFLKNSCPPTSELLGTSDRLFWEPMKVHDIRWNFEKFLVGPDGIPIMRWHHRTTVSNVKMDILSYMRRQAALGVKRK
:.........:.........:.........:.........:.........:.........:.........:.........26000
.........:.........:.........:.........:..WARNING: Found the following zero-mass residues in protein entry sp|P49908|SEPP1_HUMAN : UUUUUUUUUU
MWRSLGLALALCLLPSGGTESQDQSSLCKQPPAWSIRDQDPMLNSNGSVTVVALLQASUYLCILQASKLEDLRVKLKKEGYSNISYIVVNHQGISSRLKYTHLKNKVSEHIPVYQQEENQTDVWTLLNGSKDDFLIYDRCGRLVYHLGLPFSFLTFPYVEEAIKIAYCEKKCGNCSLTTLKDEDFCKRVSLATVDKTVETPSPHYHHEHHHNHGHQHLGSSELSENQQPGAPNAPTHPAPPGLHHHHKHKGQHRQGHPENRDMPASEDLQDLQKKLCRKRCINQLLCKLPTDSELAPRSUCCHCRHLIFEKTGSAITUQCKENLPSLCSUQGLRAEENITESCQURLPPAAUQISQQLIPTEASASURUKNQAKKUEUPSN
.......:.........:.........:.........:.........:.........27000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........28000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........29000
.........WARNING: Found the following zero-mass residues in protein entry sp|Q16881|TRXR1_HUMAN : U
MGCAEGKAVAAAAPTELQTKGKNGDGRRRSAKDHHPGKTLPENPAGFTSTATADSRALLQAYIDGHSVVIFSRSTCTRCTEVKKLFKSLCVPYFVLELDQTEDGRALEGTLSELAAETDLPVVFVKQRKIGGHGPTLKAYQEGRLQKLLKMNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCUG
:.........:.........:.........:.........:.........:.........:.........:.........:.........30000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........31000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........32000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........33000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........34000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........35000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........36000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........37000
.........:.........:.........:.........:.........:.........:.........:.........:.........:.........38000
.........:.........:.......WARNING: Found the following zero-mass residues in protein entry sp|Q9NNW7|TRXR2_HUMAN : U
MAAMAVALRGLGGRFRWRTQAVAGGVRGAARGAAAGQRDYDLLVVGGGSGGLACAKEAAQLGRKVAVVDYVEPSPQGTRWGLGGTCVNVGCIPKKLMHQAALLGGLIQDAPNYGWEVAQPVPHDWRKMAEAVQNHVKSLNWGHRVQLQDRKVKYFNIKASFVDEHTVCGVAKGGKEILLSADHIIIATGGRPRYPTHIEGALEYGITSDDIFWLKESPGKTLVVGASYVALECAGFLTGIGLDTTIMMRSIPLRGFDQQMSSMVIEHMASHGTRFLRGCAPSRVRRLPDGQLQVTWEDSTTGKEDTGTFDTVLWAIGRVPDTRSLNLEKAGVDTSPDTQKILVDSREATSVPHIYAIGDVVEGRPELTPIAIMAGRLLVQRLFGGSSDLMDYDNVPTTVFTPLEYGCVGLSEEEAVARHGQEHVEVYHAHYKPLEFTVAGRDASQCYVKMVCLREPPQLVLGLHFLGPNAGEVTQGFALGIKCGASYAQVMRTVGIHPTCSEEVVKLRISKRSGLDPTVTGCUG
..:.........:.........:.........:.........:.........:.........:.........39000
.........:WARNING: Found the following zero-mass residues in protein entry sp|Q9NZV6|MSRB1_HUMAN : U
MSFCSFFGGEVFQNHFEPGVYVCAKCGYELFSSRSKYAHSSPWPAFTETIHADSVAKRPEHNRSEALKVSCGKCGNGLGHEFLNDGPKPGQSRFUIFSSSLKFVPKGKETSASQGH
.........:.........:.........:.........:.........:.........:.........:.........:.........40000
.........:.........:.........:.........:.........:.........:.........:.........:  Total: 40800
Computing degenerate peptides for 6804 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Computing probabilities for 6973 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6973 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6973 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing probabilities for 6973 proteins.  Loop 1: 0%...20%...40%...60%...80%...100%  Loop 2: 0%...20%...40%...60%...80%...100%
Computing 6541 protein groups: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Calculating sensitivity...and error tables...
INFO: mu=0.000140747, db_size=45468307
Computing MU for 6973 proteins: 0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
INFO[16:34:53] Done                                         
Process 'ProteinProphet' finished, exit code: 0
PhilosopherDbAnnotate [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe database --annotate C:\Users\jossmith\MSFragger\Philosopher\2020-02-03-decoys-reviewed-contam-UP000005640.fas --prefix rev_
INFO[16:34:54] Executing Database  v4.1.0                   
INFO[16:34:54] Annotating the database                      
INFO[16:34:56] Done                                         
Process 'PhilosopherDbAnnotate' finished, exit code: 0
PhilosopherFilter [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe filter --sequential --mapmods --prot 0.01 --tag rev_ --pepxml C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger --protxml C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\combined.prot.xml --razor
INFO[16:34:57] Executing Filter  v4.1.0                     
INFO[16:34:57] Processing peptide identification files      
INFO[16:35:00] 1+ Charge profile                             decoy=0 target=0
INFO[16:35:00] 2+ Charge profile                             decoy=1667 target=10956
INFO[16:35:00] 3+ Charge profile                             decoy=1384 target=6681
INFO[16:35:00] 4+ Charge profile                             decoy=972 target=2222
INFO[16:35:00] 5+ Charge profile                             decoy=0 target=0
INFO[16:35:00] 6+ Charge profile                             decoy=0 target=0
INFO[16:35:00] Database search results                       ions=9884 peptides=9237 psms=23882
INFO[16:35:00] Converged to 1.00 % FDR with 11598 PSMs       decoy=117 threshold=0.7587 total=11715
INFO[16:35:00] Converged to 0.95 % FDR with 1360 Peptides    decoy=13 threshold=0.9475 total=1373
INFO[16:35:00] Converged to 0.97 % FDR with 1753 Ions        decoy=17 threshold=0.9434 total=1770
INFO[16:35:01] Protein inference results                     decoy=2974 target=3567
INFO[16:35:01] Converged to 1.19 % FDR with 253 Proteins     decoy=3 threshold=0.9717 total=256
INFO[16:35:01] Applying sequential FDR estimation            ions=1877 peptides=1452 psms=11434
INFO[16:35:01] Converged to 0.05 % FDR with 11428 PSMs       decoy=6 threshold=0.7593 total=11434
INFO[16:35:02] Converged to 0.20 % FDR with 1449 Peptides    decoy=3 threshold=0.7627 total=1452
INFO[16:35:02] Converged to 0.16 % FDR with 1874 Ions        decoy=3 threshold=0.7627 total=1877
INFO[16:35:02] Post processing identifications              
INFO[16:35:03] Mapping modifications                        
INFO[16:35:03] Assigning protein identifications to layers  
INFO[16:35:04] Processing protein inference                 
INFO[16:35:04] Synchronizing PSMs and proteins              
INFO[16:35:04] Total report numbers after FDR filtering, and post-processing  ions=1871 peptides=1446 proteins=253 psms=11423
INFO[16:35:04] Saving                                       
INFO[16:35:05] Done                                         
Process 'PhilosopherFilter' finished, exit code: 0
PhilosopherReport [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe report --decoys
INFO[16:35:05] Executing Report  v4.1.0                     
INFO[16:35:06] Creating reports                             
INFO[16:35:06] Done                                         
Process 'PhilosopherReport' finished, exit code: 0
SpecLibGen [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\Python\python -u C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\speclib\gen_con_spec_lib.py C:\Users\jossmith\MSFragger\Philosopher\2020-02-03-decoys-reviewed-contam-UP000005640.fas C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger unused C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger True unused use_easypqp noiRT;noIM 7 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',]" "--rt_lowess_fraction 0.1" delete_intermediate_files C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\filelist_speclibgen.txt
File list provided
Spectral library building
Commands to execute:
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' convert --max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types '['"'"'b'"'"','"'"'y'"'"',]' --enable_unannotated --pepxml 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\interact.pep.xml' --spectra 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML' --exclude-range -1.5,3.5 --psms JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.psmpkl --peaks JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.peakpkl
'C:\Users\jossmith\Python\Scripts\easypqp.exe' library --psmtsv 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\psm.tsv' --peptidetsv 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\peptide.tsv' --out easypqp_lib_openswath.tsv --rt_lowess_fraction 0.1 'C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\filelist_easypqp_library.txt'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
c:\users\jossmith\python\lib\site-packages\statsmodels\tools\_testing.py:19: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
  import pandas.util.testing as tm
easypqp, version 0.1.25
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.peakpkl']
Executing ['C:\\Users\\jossmith\\Python\\Scripts\\easypqp.exe', 'convert', '--max_delta_unimod', '0.02', '--max_delta_ppm', '15.0', '--fragment_types', "['b','y',]", '--enable_unannotated', '--pepxml', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\interact.pep.xml', '--spectra', 'C:\\Users\\jossmith\\Documents\\Adductomics\\ColeLabData\\211109\\PAA\\MSFragger\\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.mzML', '--exclude-range', '-1.5,3.5', '--psms', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.psmpkl', '--peaks', 'JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.peakpkl']
Info: There are psm.tsv and peptide.tsv. Will ignore --psm_fdr_threshold, --peptide_fdr_threshold, --protein_fdr_threshold, --pi0_lambda, --proteotypic, and --no-proteotypic.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.psmpkl.
Info: Reading file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.psmpkl.
Info: 11429 redundant PSMs identified after filtering with C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\psm.tsv and C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\peptide.tsv
                                            base_name  modified_peptide
0   JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1               231
1   JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2                69
2   JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3                55
3   JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_...               683
4   JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_...               333
5   JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_...               218
6   JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_D...               365
7   JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_D...               163
8   JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_D...                74
9   JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New...               461
10  JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New...               210
11  JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New...               118
12  JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_D...               340
13  JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_D...               137
14  JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_D...                89
15   JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1               636
16   JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2               331
17   JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3               149
18  JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_D...               791
19  JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_D...               445
20  JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_D...               175
21    JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1               238
22    JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2                72
23    JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3                55
24    JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1               274
25    JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2               121
26    JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3                84
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1; Peptide overlap between run and reference: 160.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2; Peptide overlap between run and reference: 46.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3; Peptide overlap between run and reference: 39.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1; Peptide overlap between run and reference: 357.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2; Peptide overlap between run and reference: 180.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3; Peptide overlap between run and reference: 121.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1; Peptide overlap between run and reference: 196.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2; Peptide overlap between run and reference: 75.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3; Peptide overlap between run and reference: 40.
c:\users\jossmith\python\lib\site-packages\statsmodels\tools\_testing.py:19: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
  import pandas.util.testing as tm
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1; Peptide overlap between run and reference: 312.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2; Peptide overlap between run and reference: 125.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3; Peptide overlap between run and reference: 71.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1; Peptide overlap between run and reference: 194.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2; Peptide overlap between run and reference: 82.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3; Peptide overlap between run and reference: 48.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1; Peptide overlap between run and reference: 398.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2; Peptide overlap between run and reference: 179.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3; Peptide overlap between run and reference: 84.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1; Peptide overlap between run and reference: 791.
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2; Peptide overlap between run and reference: 251.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3; Peptide overlap between run and reference: 125.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1; Peptide overlap between run and reference: 166.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2; Peptide overlap between run and reference: 40.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3; Peptide overlap between run and reference: 35.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1; Peptide overlap between run and reference: 172.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2; Peptide overlap between run and reference: 71.
Info: easypqp_rt_alignment_JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3; Peptide overlap between run and reference: 47.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2.peakpkl.
Info: Parsing file C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3.peakpkl.
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\cbook\__init__.py:1402: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x[:, None]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:276: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  x = x[:, np.newaxis]
c:\users\jossmith\python\lib\site-packages\matplotlib\axes\_base.py:278: FutureWarning: Support for multi-dimensional indexing (e.g. `obj[:, None]`) is deprecated and will be removed in a future version.  Convert to a numpy array before indexing instead.
  y = y[:, np.newaxis]
Info: Library successfully generated.
Done generating spectral library
2021-11-17 16:36:16,542:INFO:took 0:01:07.348808
Process 'SpecLibGen' finished, exit code: 0
PTMShepherd [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
java -Xmx25G -Dbatmass.io.libs.thermo.dir="C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\MSFragger-3.4\ext\thermo" -cp "C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\ptmshepherd-1.2.6.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\batmass-io-1.23.6.jar;C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger\shepherd.config"

PTM-Shepherd version 1.2.6(c) University of Michigan

Using Java 1.8.0_152 on 22756MB memory

Finding and caching spectral data
	Indexing data from dataset01
	Caching data from dataset01
		JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3 - 337 (657 ms, 27 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1 - 318 (383 ms, 6 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2 - 533 (520 ms, 12 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1 - 367 (201 ms, 6 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2 - 82 (80 ms, 1 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3 - 198 (55 ms, 2 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3 - 66 (13 ms, 0 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1 - 1224 (757 ms, 16 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3 - 67 (19 ms, 0 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2 - 499 (187 ms, 6 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1 - 1116 (598 ms, 7 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2 - 83 (62 ms, 0 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2 - 313 (131 ms, 1 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1 - 821 (224 ms, 4 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3 - 174 (18 ms, 1 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3 - 111 (12 ms, 1 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3 - 114 (19 ms, 0 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1 - 1706 (570 ms, 15 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2 - 223 (117 ms, 1 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1 - 585 (180 ms, 4 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1 - 561 (161 ms, 3 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3 - 270 (47 ms, 2 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2 - 174 (101 ms, 1 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2 - 805 (287 ms, 4 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3 - 104 (18 ms, 1 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1 - 398 (97 ms, 4 ms)
		JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2 - 180 (72 ms, 2 ms)
	Done caching data from dataset01
Done finding and caching spectral data
Counting MS2 scans for dataset dataset01
	11429 MS2 scans present in dataset dataset01

Creating combined histogram
	Generated histogram file for dataset dataset01 [-154 - 504]
Created combined histogram!

Running peak picking

Picked top 500 peaks

	Removed 283 peaks with insufficient PSMs
Created summary table

Annotated summary table

Mapping modifications back into PSM lists
Created modification summary
Begin localization annotation
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3 - 337 (24 ms, 149 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1 - 318 (12 ms, 92 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2 - 533 (29 ms, 174 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1 - 367 (12 ms, 103 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2 - 82 (5 ms, 23 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3 - 198 (7 ms, 57 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3 - 66 (3 ms, 17 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1 - 1224 (33 ms, 384 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3 - 67 (3 ms, 18 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2 - 499 (15 ms, 161 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1 - 1116 (30 ms, 239 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2 - 83 (3 ms, 9 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2 - 313 (8 ms, 37 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1 - 821 (21 ms, 84 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3 - 174 (5 ms, 25 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3 - 111 (4 ms, 9 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3 - 114 (4 ms, 17 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1 - 1706 (32 ms, 197 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2 - 223 (6 ms, 22 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1 - 585 (11 ms, 49 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1 - 561 (10 ms, 45 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3 - 270 (5 ms, 29 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2 - 174 (4 ms, 16 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2 - 805 (16 ms, 98 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3 - 104 (3 ms, 9 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1 - 398 (7 ms, 33 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2 - 180 (4 ms, 17 ms)
Done


Created localization reports

Begin similarity and retention time annotation
	Spectral data read into memory (277 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q3 - 337 (19 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q1 - 318 (36 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q2 - 533 (48 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q1 - 367 (58 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q2 - 82 (59 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q3 - 198 (66 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_2_New_DIA_Q3 - 66 (68 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q1 - 1224 (112 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q3 - 67 (113 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Acet_RA_2_New_DIA_Q2 - 499 (122 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_2_New_DIA_Q1 - 1116 (165 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_1_New_DIA_Q2 - 83 (166 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q2 - 313 (172 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q1 - 821 (212 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2xRA_D_New_DIA_Q3 - 174 (219 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q3 - 111 (224 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q3 - 114 (229 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q1 - 1706 (279 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q2 - 223 (282 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead1x_A_New_DIA_Q1 - 585 (296 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q1 - 561 (321 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q3 - 270 (330 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_Bead2x_C_New_DIA_Q2 - 174 (333 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_IPA_RA_2_New_DIA_Q2 - 805 (346 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q3 - 104 (348 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q1 - 398 (358 ms)
	JS-CS-211109_GroopmanJ_JS_PAA_3_NC_2_New_DIA_Q2 - 180 (361 ms)
Done

Created similarity/RT reports

Combining and cleaning reports
Writing combined table for dataset dataset01
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Process 'PTMShepherd' finished, exit code: 0
WorkspaceClean [Work dir: C:\Users\jossmith\Documents\Adductomics\ColeLabData\211109\PAA\MSFragger]
C:\Users\jossmith\MSFragger\FragPipe-17.1\fragpipe\tools\philosopher\philosopher.exe workspace --clean --nocheck
INFO[16:36:35] Executing Workspace  v4.1.0                  
INFO[16:36:35] Removing workspace                           
INFO[16:36:35] Done                                         
Process 'WorkspaceClean' finished, exit code: 0

Please cite:
(Any searches) MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics. Nat Methods 14:513 (2017)
(Any searches) Fast deisotoping algorithm and its implementation in the MSFragger search engine. J. Proteome Res. 20:498 (2021)
(Open search) Identification of modified peptides using localization-aware open search. Nat Commun. 11:4065 (2020)
(Open search) Crystal-C: A Computational Tool for Refinement of Open Search Results. J. Proteome Res. 19.6:2511 (2020)
(Open search) PTM-Shepherd: analysis and summarization of post-translational and chemical modifications from open search results. Mol Cell Proteomics 20:100018 (2020)
(Glyco/labile search) Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 17:1125 (2020)
(timsTOF PASEF) Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant. Mol Cell Proteomics 19:1575 (2020)
(PSM validation with Percolator) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4:923 (2007)
(Label-free quantification/SILAC) IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs. Mol Cell Proteomics 20:100077 (2021)
(PeptideProphet/ProteinProphet/PTMProphet/Filtering) Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 17:869 (2020)
(TMT-Integrator) Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun. 11:1723 (2020)
(DIA-Umpire) DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nat Methods 12:258 (2015)
(DIA-NN) High sensitivity dia-PASEF proteomics with DIA-NN and FragPipe. bioRxiv doi:10.1101/2021.03.08.434385 (2021)

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