Error building spectral library from MSFragger Search with timstof data | claire tonry | 2021-09-07 03:47 | |||||||||
Hi, I get the following error when I try to import the pep.xml file generated from an MSFragger search of timstof DDA data into Skyline --------------------------- Skyline --------------------------- ERROR: Could not find spectrum file 'A210120_ct_heart_FFPE_fracs_AF_F1_dda_881[.mz5|.mzML|.mzXML|.ms2|.cms2|.bms2|.pms2|_uncalibrated.mgf|_calibrated.mgf]' for search results file 'A210120_ct_heart_FFPE_fracs_AF_F1_dda_881.pepXML' in current directory, ../,../../. ERROR: Command-line: C:\Users\3053492\AppData\Local\Apps\2.0\5VYXQT5K.TNB\893P3P9W.TXB\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\BlibBuild -s -A -H -o -c 0.95 -i Skyline_Lib_Test_07092021 -S "C:\Users\3053492\AppData\Local\Temp\tmpEA60.tmp" "C:\Users\3053492\Documents\AA_FFPE_Jan21\Skyline_LibBuild\Skyline_Lib_Test_07092021.redundant.blib" Working directory: C:\Users\3053492\Documents\AA_FFPE_Jan21\Skyline_LibBuild --------------------------- OK More Info --------------------------- System.IO.IOException: ERROR: Could not find spectrum file 'A210120_ct_heart_FFPE_fracs_AF_F1_dda_881[.mz5|.mzML|.mzXML|.ms2|.cms2|.bms2|.pms2|_uncalibrated.mgf|_calibrated.mgf]' for search results file 'A210120_ct_heart_FFPE_fracs_AF_F1_dda_881.pepXML' in current directory, ../,../../. ERROR: Command-line: C:\Users\3053492\AppData\Local\Apps\2.0\5VYXQT5K.TNB\893P3P9W.TXB\skyl..tion_e4141a2a22107248_0015.0001_b2be94ac8cfe2cb4\BlibBuild -s -A -H -o -c 0.95 -i Skyline_Lib_Test_07092021 -S "C:\Users\3053492\AppData\Local\Temp\tmpEA60.tmp" "C:\Users\3053492\Documents\AA_FFPE_Jan21\Skyline_LibBuild\Skyline_Lib_Test_07092021.redundant.blib" Working directory: C:\Users\3053492\Documents\AA_FFPE_Jan21\Skyline_LibBuild at pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer, ProcessPriorityClass priorityClass) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:line 65 at pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String& commandArgs, String& messageLog, String[]& ambiguous) in C:\proj\skyline_21_1_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:line 201 at pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) in C:\proj\skyline_21_1_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:line 157 --------------------------- |
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