Starting search... Converting FASTA to Prosit input Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\B018V08C.X3X\A0JV3M5G.K2B\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx4096M -cp "C:\Users\zawadzki\AppData\Local\Apps\2.0\B018V08C.X3X\A0JV3M5G.K2B\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" edu.washington.gs.maccoss.encyclopedia.cli.ConvertFastaToPrositCSV -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\WINDOWS\Temp -i "C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\Fasta files\UP000005640_9606.fasta" -o "C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.csv" -defaultNCE 27 -defaultCharge 3 -minCharge 2 -maxCharge 3 -maxMissedCleavage 2 [16:29:28] Starting to build Prosit CSV: C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.csv [16:29:28] Reading standard formated FASTA database [16:29:37] Finished writing 2502507 peptides to Prosit CSV! [16:29:37] Finished conversion from FASTA to Prosit CSV Reusing Prosit predictions from: C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit-C8E79356182D25C7142CCC57C2BCF6B.blib Converting Prosit output to EncyclopeDIA library Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\B018V08C.X3X\A0JV3M5G.K2B\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx7898M -cp "C:\Users\zawadzki\AppData\Local\Apps\2.0\B018V08C.X3X\A0JV3M5G.K2B\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" edu.washington.gs.maccoss.encyclopedia.cli.ConvertBLIBToLibrary -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\WINDOWS\Temp -i "C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit-C8E79356182D25C7142CCC57C2BCF6B.blib" -f "C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\Fasta files\UP000005640_9606.fasta" -o "C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" [16:29:37] Indexing UP000005640_9606-z3_nce27-prosit-C8E79356182D25C7142CCC57C2BCF6B.blib ... [16:29:39] Reading BLIB file [16:29:39] BLIB doesn't contain retention times! Using SSRCalc 3 hydrophobicities as fallback. [16:29:39] Reading Fasta file UP000005640_9606.fasta [16:29:39] Reading standard formated FASTA database [16:29:39] Constructing trie from library peptides [16:29:39] Accession count histogram: [16:29:39] 0 Acc 0 Counts [16:29:39] 1 Acc 0 Counts [16:29:39] 2 Acc 0 Counts [16:29:39] 3 Acc 0 Counts [16:29:39] 4 Acc 0 Counts [16:29:39] 5 Acc 0 Counts [16:29:39] 6 Acc 0 Counts [16:29:39] 7 Acc 0 Counts [16:29:39] 8 Acc 0 Counts [16:29:39] 9 Acc 0 Counts [16:29:39] 10 Acc 0 Counts [16:29:39] 11 Acc 0 Counts [16:29:39] 12 Acc 0 Counts [16:29:39] 13 Acc 0 Counts [16:29:39] 14 Acc 0 Counts [16:29:39] 15 Acc 0 Counts [16:29:39] 16 Acc 0 Counts [16:29:39] 17 Acc 0 Counts [16:29:39] 18 Acc 0 Counts [16:29:39] 19 Acc 0 Counts [16:29:39] 20 Acc 0 Counts [16:29:39] 0 distinct protein groups found. [16:29:39] Writing library file encyclopedia_5230650906056699939.elib [16:29:39] Finished reading UP000005640_9606-z3_nce27-prosit-C8E79356182D25C7142CCC57C2BCF6B.blib Generating chromatogram library (1 of 7): Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML Running command: C:\Users\zawadzki\AppData\Local\Apps\2.0\B018V08C.X3X\A0JV3M5G.K2B\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\openlogic-openjdk-jre-8u342-b07-windows-64\bin\java.exe -Xmx7898M -jar "C:\Users\zawadzki\AppData\Local\Apps\2.0\B018V08C.X3X\A0JV3M5G.K2B\skyl..tion_9286511f3362df93_0017.0001_cdc87d1507aa7380\Tools\encyclopedia-2.12.30-executable.jar" -Duser.language=en-US -Duser.region=US -Djava.io.tmpdir=C:\WINDOWS\Temp -v2scoring "True" -i "C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML" -f "C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\Fasta files\UP000005640_9606.fasta" -l "C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\Fasta files\UP000005640_9606-z3_nce27-prosit.dlib" [16:29:47] EncyclopeDIA version 2.12.30 [16:29:47] Getting count of protein accessions... [16:29:47] Using EncyclopeDIA 2.X Scoring System [16:29:47] Indexing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML ... [16:29:47] Converting Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML ... [16:29:48] Parsed 1% [16:29:48] Parsed 2% [16:29:48] Parsed 3% [16:29:49] Parsed 4% [16:29:49] Parsed 5% [16:29:49] Parsed 6% [16:29:50] Parsed 7% [16:29:50] Parsed 8% [16:29:50] Parsed 9% [16:29:51] Parsed 10% [16:29:52] Parsed 11% [16:29:52] Parsed 12% [16:29:54] Parsed 13% [16:29:55] Parsed 14% [16:29:56] Parsed 15% [16:29:57] Parsed 16% [16:29:58] Parsed 17% [16:29:59] Parsed 18% [16:29:59] Parsed 19% [16:30:00] Parsed 20% [16:30:01] Parsed 21% [16:30:02] Parsed 22% [16:30:03] Parsed 23% [16:30:04] Parsed 24% [16:30:05] Parsed 25% [16:30:06] Parsed 26% [16:30:07] Parsed 27% [16:30:08] Parsed 28% [16:30:09] Parsed 29% [16:30:10] Parsed 30% [16:30:11] Parsed 31% [16:30:13] Parsed 32% [16:30:15] Parsed 33% [16:30:16] Parsed 34% [16:30:17] Parsed 35% [16:30:18] Parsed 36% [16:30:19] Parsed 37% [16:30:20] Parsed 38% [16:30:22] Parsed 39% [16:30:24] Parsed 40% [16:30:25] Parsed 41% [16:30:26] Parsed 42% [16:30:27] Parsed 43% [16:30:28] Parsed 44% [16:30:30] Parsed 45% [16:30:31] Parsed 46% [16:30:33] Parsed 47% [16:30:34] Parsed 48% [16:30:36] Parsed 49% [16:30:37] Parsed 50% [16:30:38] Parsed 51% [16:30:39] Parsed 52% [16:30:42] Parsed 53% [16:30:43] Parsed 54% [16:30:44] Parsed 55% [16:30:45] Parsed 56% [16:30:46] Parsed 57% [16:30:47] Parsed 58% [16:30:49] Parsed 59% [16:30:51] Parsed 60% [16:30:52] Parsed 61% [16:30:53] Parsed 62% [16:30:54] Parsed 63% [16:30:55] Parsed 64% [16:30:57] Parsed 65% [16:30:58] Parsed 66% [16:30:59] Parsed 67% [16:31:00] Parsed 68% [16:31:02] Parsed 69% [16:31:03] Parsed 70% [16:31:05] Parsed 71% [16:31:07] Parsed 72% [16:31:08] Parsed 73% [16:31:09] Parsed 74% [16:31:10] Parsed 75% [16:31:11] Parsed 76% [16:31:13] Parsed 77% [16:31:15] Parsed 78% [16:31:16] Parsed 79% [16:31:17] Parsed 80% [16:31:18] Parsed 81% [16:31:19] Parsed 82% [16:31:21] Parsed 83% [16:31:22] Parsed 84% [16:31:24] Parsed 85% [16:31:25] Parsed 86% [16:31:26] Parsed 87% [16:31:27] Parsed 88% [16:31:29] Parsed 89% [16:31:32] Parsed 90% [16:31:34] Parsed 91% [16:31:35] Parsed 92% [16:31:36] Parsed 93% [16:31:37] Parsed 94% [16:31:38] Parsed 95% [16:31:38] Parsed 96% [16:31:39] Parsed 97% [16:31:40] Parsed 98% [16:31:40] Parsed 99% [16:31:41] Finalizing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.dia ... [16:31:42] Finished writing Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.dia! [16:31:42] Input File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML [16:31:42] Library File: UP000005640_9606-z3_nce27-prosit.dlib [16:31:42] Result File: Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.elib [16:31:42] Parameters: [16:31:42] -fixed -frag CID -ptol 10.0 -ftol 10.0 -lftol 10.0 -ptolunits PPM -ftolunits PPM -lftolunits PPM -poffset 0.0 -foffset 0.0 -enzyme Trypsin -percolatorThreshold 0.01 -percolatorVersion v3-01 -percolatorTrainingIterations 10 -percolatorTrainingSetSize 500000 -percolatorTrainingFDR 0.0 -acquisition DIA -numberOfThreadsUsed 12 -expectedPeakWidth 25.0 -precursorWindowSize -1.0 -numberOfQuantitativePeaks 5 -minNumOfQuantitativePeaks 3 -topNTargetsUsed -1 -quantifyAcrossSamples true -numberOfExtraDecoyLibrariesSearched 0.0 -verifyModificationIons true -minIntensity -1.0 -scoringBreadthType recal -localizationModification none -rtWindowInMin -1.0 -filterPeaklists false -precursorIsolationRangeFile none -percolatorModelFile none [16:31:42] Converting files... [16:31:42] Calculating features... [16:31:42] Processing precursors scans... [16:31:42] Constructing writer for C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [16:31:42] Processing 398.4 to 400.4 m/z, (3.9095361 second duty cycle) [16:31:42] Processing 400.4 to 402.4 m/z, (1.9547969 second duty cycle) [16:31:43] Processing 402.4 to 404.4 m/z, (1.9547969 second duty cycle) [16:31:43] Processing 404.4 to 406.4 m/z, (1.954797 second duty cycle) [16:31:43] Processing 406.4 to 408.4 m/z, (1.9547969 second duty cycle) [16:31:44] Processing 408.4 to 410.4 m/z, (1.954797 second duty cycle) [16:31:44] Processing 410.4 to 412.4 m/z, (1.9547969 second duty cycle) [16:31:44] Processing 412.4 to 414.4 m/z, (1.9547969 second duty cycle) [16:31:44] Processing 414.4 to 416.4 m/z, (1.9547967 second duty cycle) [16:31:44] Processing 416.4 to 418.4 m/z, (1.954797 second duty cycle) [16:31:45] Processing 418.4 to 420.4 m/z, (1.954797 second duty cycle) [16:31:45] Processing 420.4 to 422.4 m/z, (1.9547969 second duty cycle) [16:31:45] Processing 422.4 to 424.4 m/z, (1.9547969 second duty cycle) [16:31:45] Processing 424.4 to 426.4 m/z, (1.9547971 second duty cycle) [16:31:45] Processing 426.4 to 428.4 m/z, (1.954797 second duty cycle) [16:31:46] Processing 428.4 to 430.4 m/z, (1.954797 second duty cycle) [16:31:46] Processing 430.4 to 432.4 m/z, (1.9547969 second duty cycle) [16:31:46] Processing 432.4 to 434.4 m/z, (1.9547971 second duty cycle) [16:31:46] Processing 434.4 to 436.4 m/z, (1.9547971 second duty cycle) [16:31:47] Processing 436.4 to 438.4 m/z, (1.954797 second duty cycle) [16:31:47] Processing 438.4 to 440.5 m/z, (1.954797 second duty cycle) [16:31:47] Processing 440.5 to 442.5 m/z, (1.9547971 second duty cycle) [16:31:47] Processing 442.5 to 444.5 m/z, (1.9547971 second duty cycle) [16:31:47] Processing 444.5 to 446.5 m/z, (1.954797 second duty cycle) [16:31:47] Processing 446.5 to 448.5 m/z, (1.954797 second duty cycle) [16:31:47] Processing 448.5 to 450.5 m/z, (1.9547973 second duty cycle) [16:31:48] Processing 450.5 to 452.5 m/z, (1.9547971 second duty cycle) [16:31:48] Processing 452.5 to 454.5 m/z, (1.9547971 second duty cycle) [16:31:48] Processing 454.5 to 456.5 m/z, (1.9547971 second duty cycle) [16:31:48] Processing 456.5 to 458.5 m/z, (1.9548858 second duty cycle) [16:31:48] Processing 458.5 to 460.5 m/z, (1.9548858 second duty cycle) [16:31:48] Processing 460.5 to 462.5 m/z, (1.9548856 second duty cycle) [16:31:49] Processing 462.5 to 464.5 m/z, (1.9548856 second duty cycle) [16:31:49] Processing 464.5 to 466.5 m/z, (1.9548858 second duty cycle) [16:31:49] Processing 466.5 to 468.5 m/z, (1.9548858 second duty cycle) [16:31:49] Processing 468.5 to 470.5 m/z, (1.9548858 second duty cycle) [16:31:49] Processing 470.5 to 472.5 m/z, (1.9548858 second duty cycle) [16:31:49] Processing 472.5 to 474.5 m/z, (1.9548458 second duty cycle) [16:31:50] Processing 474.5 to 476.5 m/z, (1.9548671 second duty cycle) [16:31:50] Processing 476.5 to 478.5 m/z, (1.9548455 second duty cycle) [16:31:50] Processing 478.5 to 480.5 m/z, (1.9548671 second duty cycle) [16:31:50] Processing 480.5 to 482.5 m/z, (1.9548455 second duty cycle) [16:31:51] Processing 482.5 to 484.5 m/z, (1.9548671 second duty cycle) [16:31:51] Processing 484.5 to 486.5 m/z, (1.9548455 second duty cycle) [16:31:51] Processing 486.5 to 488.5 m/z, (1.9548671 second duty cycle) [16:31:51] Processing 488.5 to 490.5 m/z, (1.9548458 second duty cycle) [16:31:51] Processing 490.5 to 492.5 m/z, (1.9548671 second duty cycle) [16:31:51] Processing 492.5 to 494.5 m/z, (1.9548455 second duty cycle) [16:31:52] Processing 494.5 to 496.5 m/z, (1.9548671 second duty cycle) [16:31:52] Processing 496.5 to 498.5 m/z, (1.9548459 second duty cycle) [16:31:52] Processing 498.5 to 500.5 m/z, (1.9548672 second duty cycle) [16:31:52] Processing 500.5 to 502.5 m/z, (3.909591 second duty cycle) [16:31:52] Sorting results into C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [16:31:52] Sorted feature file in 0.03 seconds wall clock time [16:31:52] File size check: 0 vs 0 (diff: 0) Removing temp file C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt.unsorted [16:31:52] 0 total peptides processed. [16:31:52] Running Percolator... [16:31:52] Executing [cmd /c C:\WINDOWS\Temp\tmp251.java\Percolator-v3-01-1345106419958614304.exe --results-peptides C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt] [16:31:53] Percolator version 3.01.nightly-13-655e4c7-dirty, Build Date May 18 2017 15:22:44 [16:31:53] Copyright (c) 2006-9 University of Washington. All rights reserved. [16:31:53] Written by Lukas Käll (lukall@u.washington.edu) in the [16:31:53] Department of Genome Sciences at the University of Washington. [16:31:53] Issued command: [16:31:53] C:\WINDOWS\Temp\tmp251.java\Percolator-v3-01-1345106419958614304.exe --results-peptides C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt --weights C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.txt.1.weights --decoy-results-peptides C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.encyclopedia.decoy.txt -y --maxiter 3 --no-terminate -N 500000 --testFDR 0.01 --trainFDR 0.0 C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [16:31:53] Started Sat Jul 13 16:31:53 2024 [16:31:53] Hyperparameters: selectionFdr=0, Cpos=0, Cneg=0, maxNiter=3 [16:31:53] Reading tab-delimited input from datafile C:\Users\zawadzki\OneDrive - Vertex Pharmaceuticals\Documents\HeLa QC\DIA\elib_chrom\Inst-Exploris480_Date-2024JUL09_Evts-A2_Meth-90min-400_500mz_DIA_Cond-50cm_01.mzML.features.txt [16:31:53] [16:31:53] WARNING: Tab delimited input does not contain ScanNr column, [16:31:53] scan numbers will be assigned automatically. [16:31:53] [16:31:53] Features: [16:31:53] [16:31:53] ERROR: Reading tab file, too few features present. [16:31:53] No-terminate flag set: ignoring error and using a pseudo-feature of zeroes. [16:31:53] Exception caught: ERROR: Reading tab file, error reading PSM on line 2. Could not read PSMid. [16:31:53] [16:31:53] Fatal Error: Percolator exited with non-zero status: 1 [16:31:53] Sorry, not feeling well today! Try again tomorrow! [16:31:53] Encountered Fatal Error! [16:31:53] edu.washington.gs.maccoss.encyclopedia.utils.EncyclopediaException: Percolator exited with non-zero status: 1 at edu.washington.gs.maccoss.encyclopedia.algorithms.percolator.PercolatorExecutor.checkResult(PercolatorExecutor.java:194) at edu.washington.gs.maccoss.encyclopedia.algorithms.percolator.PercolatorExecutor.executePercolatorTSV(PercolatorExecutor.java:129) at edu.washington.gs.maccoss.encyclopedia.Encyclopedia.percolatePeptides(Encyclopedia.java:468) at edu.washington.gs.maccoss.encyclopedia.Encyclopedia.runTop5Search(Encyclopedia.java:265) at edu.washington.gs.maccoss.encyclopedia.Encyclopedia.runSearch(Encyclopedia.java:252) at edu.washington.gs.maccoss.encyclopedia.Encyclopedia.runSearch(Encyclopedia.java:242) at edu.washington.gs.maccoss.encyclopedia.Encyclopedia.main(Encyclopedia.java:173)