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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
http://fragpipe.nesvilab.org
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Error as MsFragger' finished, exit code: 1 #284

Closed Microbiomiao closed 3 years ago

Microbiomiao commented 3 years ago

Hi, I am new to MSFragger and would like to use it for my research work. I got an error message as follow: ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 23.927 MIN* ***TOTAL TIME 163.672 MIN**** STARTED: slice 1 of 3 ['C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx6G', WindowsPath('C:/MSFragger/MSFragger-3.1/MSFragger-3.1.jar'), 'fragger.params', WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_01.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_02.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_03.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_01.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_02.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_03.mzBIN_calibrated'), '--partial', '0'] Traceback (most recent call last): File "C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\msfragger_pep_split.py", line 470, in main() File "C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\msfragger_pep_split.py", line 459, in main run_msfragger(calibrate_mzBIN if calibrate_mass in [1, 2] else infiles_name) File "C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\msfragger_pep_split.py", line 149, in run_msfragger subprocess.run(list(map(os.fspath, cmd)), cwd=cwd, check=True) File "C:\Users\User\anaconda3\lib\subprocess.py", line 512, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx6G', 'C:\MSFragger\MSFragger-3.1\MSFragger-3.1.jar', 'fragger.params', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_01.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_02.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_03.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_01.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_02.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_03.mzBIN_calibrated', '--partial', '0']' returned non-zero exit status 1. Process 'MsFragger' finished, exit code: 1 Process returned non-zero exit code, stoppingMsFragger move pepxml C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_7_phos_01.pepXML D:\ADP-ribo\7_1\iPSC_7_phos_01.pepXML


Cancelling 58 remaining tasks
Processing interrupted, stopping MsFragger move pepxml

Does anyone have ideas about how to solve this problem? 
Shall I provide any other information ?
Thank you very much.
guoci commented 3 years ago

@Microbiomiao please post the full log

Microbiomiao commented 3 years ago

Hi Guoci,

Full log as follow:

System OS: Windows 10, Architecture: AMD64 Java Info: 1.8.0_242, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 14.0 MSFragger version 3.1 Philosopher version 3.3.12 (build 1604525264)

LCMS files: Experiment/Group: 7_1

73 commands to execute: WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MsFragger [Work dir: D:\ADP-ribo] C:\Users\User\anaconda3\pythonw.exe C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\msfragger_pep_split.py 3 "C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx6G" C:\MSFragger\MSFragger-3.1\MSFragger-3.1.jar D:\ADP-ribo\fragger.params D:\ADP-ribo\iPSC_7_phos_01.raw D:\ADP-ribo\iPSC_7_phos_02.raw D:\ADP-ribo\iPSC_7_phos_03.raw D:\ADP-ribo\iPSC_PT_phos_01.raw D:\ADP-ribo\iPSC_PT_phos_02.raw D:\ADP-ribo\iPSC_PT_phos_03.raw MsFragger move pepxml C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_7_phos_01.pepXML D:\ADP-ribo\7_1\iPSC_7_phos_01.pepXML MsFragger move pepxml C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_7_phos_02.pepXML D:\ADP-ribo\7_2\iPSC_7_phos_02.pepXML MsFragger move pepxml C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_7_phos_03.pepXML D:\ADP-ribo\7_3\iPSC_7_phos_03.pepXML MsFragger move pepxml C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_PT_phos_01.pepXML D:\ADP-ribo\PT_1\iPSC_PT_phos_01.pepXML MsFragger move pepxml C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_PT_phos_02.pepXML D:\ADP-ribo\PT_2\iPSC_PT_phos_02.pepXML MsFragger move pepxml C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_PT_phos_03.pepXML D:\ADP-ribo\PT_3\iPSC_PT_phos_03.pepXML PeptideProphet: Workspace init [Work dir: D:\ADP-ribo\7_3\fragpipe-iPSC_7_phos_03.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ADP-ribo\PT_1\fragpipe-iPSC_PT_phos_01.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ADP-ribo\PT_3\fragpipe-iPSC_PT_phos_03.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ADP-ribo\7_1\fragpipe-iPSC_7_phos_01.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ADP-ribo\7_2\fragpipe-iPSC_7_phos_02.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet: Workspace init [Work dir: D:\ADP-ribo\PT_2\fragpipe-iPSC_PT_phos_02.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck PeptideProphet [Work dir: D:\ADP-ribo\7_3\fragpipe-iPSC_7_phos03.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas ..\iPSC_7_phos_03.pepXML PeptideProphet [Work dir: D:\ADP-ribo\PT_1\fragpipe-iPSC_PT_phos01.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas ..\iPSC_PT_phos_01.pepXML PeptideProphet [Work dir: D:\ADP-ribo\PT_3\fragpipe-iPSC_PT_phos03.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas ..\iPSC_PT_phos_03.pepXML PeptideProphet [Work dir: D:\ADP-ribo\7_1\fragpipe-iPSC_7_phos01.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas ..\iPSC_7_phos_01.pepXML PeptideProphet [Work dir: D:\ADP-ribo\7_2\fragpipe-iPSC_7_phos02.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas ..\iPSC_7_phos_02.pepXML PeptideProphet [Work dir: D:\ADP-ribo\PT_2\fragpipe-iPSC_PT_phos02.pepXML-temp] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --decoyprobs --ppm --accmass --nonparam --expectscore --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas ..\iPSC_PT_phos_02.pepXML PeptideProphet: Delete temp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete D:\ADP-ribo\7_3\fragpipe-iPSC_7_phos_03.pepXML-temp PeptideProphet: Delete temp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete D:\ADP-ribo\PT_1\fragpipe-iPSC_PT_phos_01.pepXML-temp PeptideProphet: Delete temp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete D:\ADP-ribo\PT_3\fragpipe-iPSC_PT_phos_03.pepXML-temp PeptideProphet: Delete temp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete D:\ADP-ribo\7_1\fragpipe-iPSC_7_phos_01.pepXML-temp PeptideProphet: Delete temp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete D:\ADP-ribo\7_2\fragpipe-iPSC_7_phos_02.pepXML-temp PeptideProphet: Delete temp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileDelete D:\ADP-ribo\PT_2\fragpipe-iPSC_PT_phos_02.pepXML-temp Rewrite pepxml [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\PT_3\interact-iPSC_PT_phos_03.pep.xml D:\ADP-ribo\iPSC_PT_phos_03.raw Rewrite pepxml [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\PT_2\interact-iPSC_PT_phos_02.pep.xml D:\ADP-ribo\iPSC_PT_phos_02.raw Rewrite pepxml [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\7_1\interact-iPSC_7_phos_01.pep.xml D:\ADP-ribo\iPSC_7_phos_01.raw Rewrite pepxml [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\PT_1\interact-iPSC_PT_phos_01.pep.xml D:\ADP-ribo\iPSC_PT_phos_01.raw Rewrite pepxml [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\7_3\interact-iPSC_7_phos_03.pep.xml D:\ADP-ribo\iPSC_7_phos_03.raw Rewrite pepxml [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\7_2\interact-iPSC_7_phos_02.pep.xml D:\ADP-ribo\iPSC_7_phos_02.raw PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\ADP-ribo\PT1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev --pepxml D:\ADP-ribo\PT_1 PhilosopherFilter [Work dir: D:\ADP-ribo\PT2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev --pepxml D:\ADP-ribo\PT_2 PhilosopherFilter [Work dir: D:\ADP-ribo\71] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev --pepxml D:\ADP-ribo\7_1 PhilosopherFilter [Work dir: D:\ADP-ribo\73] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev --pepxml D:\ADP-ribo\7_3 PhilosopherFilter [Work dir: D:\ADP-ribo\72] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev --pepxml D:\ADP-ribo\7_2 PhilosopherFilter [Work dir: D:\ADP-ribo\PT3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --tag rev --pepxml D:\ADP-ribo\PT_3 PhilosopherReport [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\PT3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherAbacus [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe abacus --razor --reprint --tag rev --protein PT_1 PT_2 7_1 7_3 7_2 PT_3 IonQuant [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -Xmx6G -Dlibs.bruker.dir="C:\MSFragger\MSFragger-3.1\ext\bruker" -Dlibs.thermo.dir="C:\MSFragger\MSFragger-3.1\ext\thermo" -cp "C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\ionquant-1.4.6.jar;C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\batmass-io-1.19.5.jar" ionquant.IonQuant --threads 15 --ionmobility 0 --mbr 1 --proteinquant 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 1.0 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 1 --writeindex 0 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm PT_1\psm.tsv --psm PT_2\psm.tsv --psm 7_1\psm.tsv --psm 7_3\psm.tsv --psm 7_2\psm.tsv --psm PT_3\psm.tsv --multidir . --specdir D:\ADP-ribo 7_3\iPSC_7_phos_03.pepXML PT_1\iPSC_PT_phos_01.pepXML PT_3\iPSC_PT_phos_03.pepXML 7_1\iPSC_7_phos_01.pepXML 7_2\iPSC_7_phos_02.pepXML PT_2\iPSC_PT_phos_02.pepXML WorkspaceClean [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [D:\ADP-ribo]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\7_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\7_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\PT_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\7_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\PT_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\PT_3]
    Cmd: [MsFragger], Work dir: [D:\ADP-ribo]
    Cmd: [PeptideProphet], Work dir: [D:\ADP-ribo]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\ADP-ribo]
    Cmd: [PhilosopherFilter], Work dir: [D:\ADP-ribo]
    Cmd: [PhilosopherReport], Work dir: [D:\ADP-ribo]
    Cmd: [PhilosopherAbacus], Work dir: [D:\ADP-ribo]
    Cmd: [IonQuant], Work dir: [D:\ADP-ribo]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\7_2]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\7_3]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\PT_1]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\7_1]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\PT_2]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\PT_3]

# FragPipe v14.0ui state cache

crystalc.run-crystalc=false
database.db-path=C\:\\MaxQuant\\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\MSFragger\\MSFragger-3.1\\MSFragger-3.1.jar
fragpipe-config.bin-philosopher=C\:\\Users\\User\\Downloads\\FragPipe-jre-14.0\\fragpipe\\lib\\..\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\User\\anaconda3\\pythonw.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=1
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=1
ionquant.requantify=1
ionquant.rttol=1.0
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=5
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=0.1
msfragger.fragment_mass_units=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
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=5
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=trypsin
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=3
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-10
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=10
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=P
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=trypsin
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; 42.010600,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; 57.021464,C (cysteine),true,-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 ,false,-1; 0.000000,J,false,-1; 0.000000,O,false,-1; 0.000000,U,false,-1; 0.000000,X,false,-1; 0.000000,Z,false,-1
msfragger.table.var-mods=15.994900,M,true,3; 42.010600,[^,true,1; 79.966330,STY,true,3; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 541.061100,DKER,true,1; 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_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --prot 0.01
phi-report.pep-level-summary=false
phi-report.print-decoys=false
phi-report.run-report=true
protein-prophet.cmd-opts=--maxppmdiff 2000000
protein-prophet.run-protein-prophet=false
ptmprophet.cmdline=--keepold --static --em 1 --nions b --mods STY\:79.966331,M\:15.9949 --minprob 0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
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_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=-1
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.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
workdir=D\:\\ADP-ribo
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=6
workflow.threads=15

WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[17:20:48] Executing Workspace v3.3.12
INFO[17:20:48] Removing workspace
WARN[17:20:48] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[17:20:48] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[17:20:49] Executing Workspace v3.3.12
INFO[17:20:49] Creating workspace
INFO[17:20:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[17:20:49] Executing Workspace v3.3.12
INFO[17:20:49] Removing workspace
WARN[17:20:49] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[17:20:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:20:49] Executing Workspace v3.3.12
INFO[17:20:49] Creating workspace
INFO[17:20:49] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:20:50] Executing Workspace v3.3.12
INFO[17:20:50] Removing workspace
WARN[17:20:50] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[17:20:50] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:20:50] Executing Workspace v3.3.12
INFO[17:20:50] Creating workspace
INFO[17:20:50] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:20:50] Executing Workspace v3.3.12
INFO[17:20:50] Removing workspace
WARN[17:20:50] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[17:20:50] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[17:20:50] Executing Workspace v3.3.12
INFO[17:20:50] Creating workspace
Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:20:57] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[17:20:57] Executing Workspace v3.3.12
INFO[17:20:57] Removing workspace
WARN[17:20:57] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[17:20:57] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:20:57] Executing Workspace v3.3.12
INFO[17:20:58] Creating workspace
INFO[17:20:58] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[17:20:58] Executing Workspace v3.3.12
INFO[17:20:58] Removing workspace
INFO[17:20:58] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:20:58] Executing Workspace v3.3.12
INFO[17:20:58] Creating workspace
INFO[17:20:58] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:20:58] Executing Workspace v3.3.12
INFO[17:20:58] Removing workspace
WARN[17:20:58] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[17:20:58] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[17:20:58] Executing Workspace v3.3.12
INFO[17:20:58] Creating workspace
INFO[17:20:58] Done
MsFragger [Work dir: D:\ADP-ribo] C:\Users\User\anaconda3\pythonw.exe C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\msfragger_pep_split.py 3 "C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx6G" C:\MSFragger\MSFragger-3.1\MSFragger-3.1.jar D:\ADP-ribo\fragger.params D:\ADP-ribo\iPSC_7_phos_01.raw D:\ADP-ribo\iPSC_7_phos_02.raw D:\ADP-ribo\iPSC_7_phos_03.raw D:\ADP-ribo\iPSC_PT_phos_01.raw D:\ADP-ribo\iPSC_PT_phos_02.raw D:\ADP-ribo\iPSC_PT_phos_03.raw ['C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx6G', WindowsPath('C:/MSFragger/MSFragger-3.1/MSFragger-3.1.jar'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/fragger.params'), '--split1', WindowsPath('D:/ADP-ribo/iPSC_7_phos_01.raw'), WindowsPath('D:/ADP-ribo/iPSC_7_phos_02.raw'), WindowsPath('D:/ADP-ribo/iPSC_7_phos_03.raw'), WindowsPath('D:/ADP-ribo/iPSC_PT_phos_01.raw'), WindowsPath('D:/ADP-ribo/iPSC_PT_phos_02.raw'), WindowsPath('D:/ADP-ribo/iPSC_PT_phos_03.raw')] MSFragger version MSFragger-3.1 Batmass-IO version 1.19.5 timsdata library version timsdata-2-7-0 (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_242, OpenJDK 64-Bit Server VM, JVM started with 5 GB memory Checking database... Checking D:\ADP-ribo\iPSC_7_phos_01.raw... Checking D:\ADP-ribo\iPSC_7_phos_02.raw... Checking D:\ADP-ribo\iPSC_7_phos_03.raw... Checking D:\ADP-ribo\iPSC_PT_phos_01.raw... Checking D:\ADP-ribo\iPSC_PT_phos_02.raw... Checking D:\ADP-ribo\iPSC_PT_phos_03.raw... Checking if the data is low resolution MS/MS... ***FIRST SEARCH**** Parameters: num_threads = 15 database_name = 2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 100.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false 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_cutafter = KR search_enzyme_butnotafter = P num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 2 deisotope = 1 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 = 150 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 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_03 = 79.966330 STY 2 add_A_alanine = 0.000000 add_C_cysteine = 57.021464 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_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 = 42.0106 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_V_valine = 0.000000 add_W_tryptophan = 0.000000 add_Y_tyrosine = 0.000000 Selected fragment index width 0.50 Da. 5580783570 fragments to be searched in 33 slices (83.16 GB total) Operating on slice 1 of 33: Fragment index slice generated in 2.61 s

  1. iPSC_7_phos_01.raw 50.8 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 27253 spectra/s] 2.2s
  2. iPSC_7_phos_02.raw 51.0 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 26317 spectra/s] 2.2s
  3. iPSC_7_phos_03.raw 51.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 28954 spectra/s] 2.0s
  4. iPSC_PT_phos_01.raw 50.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 28388 spectra/s] 2.1s
  5. iPSC_PT_phos_02.raw 52.2 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 27721 spectra/s] 2.1s
  6. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 25404 spectra/s] 2.4s Operating on slice 2 of 33: Fragment index slice generated in 1.94 s
  7. iPSC_7_phos_01.raw 33.2 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 27980 spectra/s] 2.1s
  8. iPSC_7_phos_02.raw 33.0 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 29107 spectra/s] 2.0s
  9. iPSC_7_phos_03.raw 33.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 25651 spectra/s] 2.3s
  10. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.3 s [progress: 58422/58422 (100%) - 28223 spectra/s] 2.1s
  11. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 26202 spectra/s] 2.3s
  12. iPSC_PT_phos_03.raw 34.4 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 28755 spectra/s] 2.1s Operating on slice 3 of 33: Fragment index slice generated in 1.63 s
  13. iPSC_7_phos_01.raw 32.9 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 31894 spectra/s] 1.8s
  14. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 30825 spectra/s] 1.9s
  15. iPSC_7_phos_03.raw 33.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 32018 spectra/s] 1.8s
  16. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.4 s [progress: 58422/58422 (100%) - 31855 spectra/s] 1.8s
  17. iPSC_PT_phos_02.raw 33.5 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 31392 spectra/s] 1.9s
  18. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 31533 spectra/s] 1.9s Operating on slice 4 of 33: Fragment index slice generated in 1.53 s
  19. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 35537 spectra/s] 1.7s
  20. iPSC_7_phos_02.raw 33.0 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 33828 spectra/s] 1.7s
  21. iPSC_7_phos_03.raw 33.2 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 35122 spectra/s] 1.7s
  22. iPSC_PT_phos_01.raw 33.0 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 35300 spectra/s] 1.7s
  23. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 36653 spectra/s] 1.6s
  24. iPSC_PT_phos_03.raw 33.7 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 36551 spectra/s] 1.6s Operating on slice 5 of 33: Fragment index slice generated in 1.56 s
  25. iPSC_7_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 41447 spectra/s] 1.4s
  26. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 38912 spectra/s] 1.5s
  27. iPSC_7_phos_03.raw 33.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 39816 spectra/s] 1.5s
  28. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 38537 spectra/s] 1.5s
  29. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 40318 spectra/s] 1.5s
  30. iPSC_PT_phos_03.raw 33.8 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 37398 spectra/s] 1.6s Operating on slice 6 of 33: Fragment index slice generated in 1.49 s
  31. iPSC_7_phos_01.raw 32.7 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 41071 spectra/s] 1.4s
  32. iPSC_7_phos_02.raw 32.7 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 41894 spectra/s] 1.4s
  33. iPSC_7_phos_03.raw 33.2 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 41447 spectra/s] 1.4s
  34. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.4 s [progress: 58422/58422 (100%) - 43827 spectra/s] 1.3s
  35. iPSC_PT_phos_02.raw 33.6 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 38237 spectra/s] 1.6s
  36. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 40907 spectra/s] 1.5s Operating on slice 7 of 33: Fragment index slice generated in 1.50 s
  37. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 44022 spectra/s] 1.3s
  38. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 41746 spectra/s] 1.4s
  39. iPSC_7_phos_03.raw 33.3 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 42901 spectra/s] 1.4s
  40. iPSC_PT_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 43308 spectra/s] 1.3s
  41. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 39671 spectra/s] 1.5s
  42. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 45177 spectra/s] 1.3s Operating on slice 8 of 33: Fragment index slice generated in 1.48 s
  43. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 44589 spectra/s] 1.3s
  44. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 44316 spectra/s] 1.3s
  45. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 40116 spectra/s] 1.5s
  46. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.3 s [progress: 58422/58422 (100%) - 42800 spectra/s] 1.4s
  47. iPSC_PT_phos_02.raw 33.6 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 44731 spectra/s] 1.3s
  48. iPSC_PT_phos_03.raw 33.4 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 41331 spectra/s] 1.4s Operating on slice 9 of 33: Fragment index slice generated in 1.55 s
  49. iPSC_7_phos_01.raw 32.7 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 44320 spectra/s] 1.3s
  50. iPSC_7_phos_02.raw 33.1 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 43532 spectra/s] 1.4s
  51. iPSC_7_phos_03.raw 33.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 42901 spectra/s] 1.4s
  52. iPSC_PT_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 41405 spectra/s] 1.4s
  53. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 44000 spectra/s] 1.3s
  54. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 43373 spectra/s] 1.4s Operating on slice 10 of 33: Fragment index slice generated in 1.43 s
  55. iPSC_7_phos_01.raw 32.6 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 46200 spectra/s] 1.3s
  56. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 47681 spectra/s] 1.2s
  57. iPSC_7_phos_03.raw 32.9 s | deisotoping 0.4 s [progress: 58689/58689 (100%) - 48224 spectra/s] 1.2s
  58. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 43021 spectra/s] 1.4s
  59. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 42154 spectra/s] 1.4s
  60. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 45211 spectra/s] 1.3s Operating on slice 11 of 33: Fragment index slice generated in 1.48 s
  61. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 42898 spectra/s] 1.4s
  62. iPSC_7_phos_02.raw 32.8 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 44889 spectra/s] 1.3s
  63. iPSC_7_phos_03.raw 32.9 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 39548 spectra/s] 1.5s
  64. iPSC_PT_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 47966 spectra/s] 1.2s
  65. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 45174 spectra/s] 1.3s
  66. iPSC_PT_phos_03.raw 33.4 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 48675 spectra/s] 1.2s Operating on slice 12 of 33: Fragment index slice generated in 1.46 s
  67. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 43630 spectra/s] 1.3s
  68. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 46886 spectra/s] 1.3s
  69. iPSC_7_phos_03.raw 33.2 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 47292 spectra/s] 1.2s
  70. iPSC_PT_phos_01.raw 32.6 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 41463 spectra/s] 1.4s
  71. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 45591 spectra/s] 1.3s
  72. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 40300 spectra/s] 1.5s Operating on slice 13 of 33: Fragment index slice generated in 1.41 s
  73. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 48486 spectra/s] 1.2s
  74. iPSC_7_phos_02.raw 33.2 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 47451 spectra/s] 1.2s
  75. iPSC_7_phos_03.raw 33.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 47949 spectra/s] 1.2s
  76. iPSC_PT_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 44192 spectra/s] 1.3s
  77. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 43293 spectra/s] 1.4s
  78. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 48994 spectra/s] 1.2s Operating on slice 14 of 33: Fragment index slice generated in 1.47 s
  79. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 48050 spectra/s] 1.2s
  80. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 50887 spectra/s] 1.2s
  81. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.4 s [progress: 58689/58689 (100%) - 51527 spectra/s] 1.1s
  82. iPSC_PT_phos_01.raw 32.7 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 45678 spectra/s] 1.3s
  83. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 48620 spectra/s] 1.2s
  84. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 48320 spectra/s] 1.2s Operating on slice 15 of 33: Fragment index slice generated in 1.45 s
  85. iPSC_7_phos_01.raw 32.7 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 50397 spectra/s] 1.2s
  86. iPSC_7_phos_02.raw 32.8 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 50843 spectra/s] 1.2s
  87. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.3 s [progress: 58689/58689 (100%) - 49318 spectra/s] 1.2s
  88. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 50105 spectra/s] 1.2s
  89. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 54077 spectra/s] 1.1s
  90. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 51003 spectra/s] 1.2s Operating on slice 16 of 33: Fragment index slice generated in 1.40 s
  91. iPSC_7_phos_01.raw 32.9 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 53032 spectra/s] 1.1s
  92. iPSC_7_phos_02.raw 33.0 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 54455 spectra/s] 1.1s
  93. iPSC_7_phos_03.raw 33.2 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 57202 spectra/s] 1.0s
  94. iPSC_PT_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 46626 spectra/s] 1.3s
  95. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 53108 spectra/s] 1.1s
  96. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 51003 spectra/s] 1.2s Operating on slice 17 of 33: Fragment index slice generated in 1.44 s
  97. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 53032 spectra/s] 1.1s
  98. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 53859 spectra/s] 1.1s
  99. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.4 s [progress: 58689/58689 (100%) - 51983 spectra/s] 1.1s
  100. iPSC_PT_phos_01.raw 32.7 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 49976 spectra/s] 1.2s
  101. iPSC_PT_phos_02.raw 33.5 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 53395 spectra/s] 1.1s
  102. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 46155 spectra/s] 1.3s Operating on slice 18 of 33: Fragment index slice generated in 1.42 s
  103. iPSC_7_phos_01.raw 32.7 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 53080 spectra/s] 1.1s
  104. iPSC_7_phos_02.raw 32.8 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 54355 spectra/s] 1.1s
  105. iPSC_7_phos_03.raw 33.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 58281 spectra/s] 1.0s
  106. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 46589 spectra/s] 1.3s
  107. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 58163 spectra/s] 1.0s
  108. iPSC_PT_phos_03.raw 34.3 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 51309 spectra/s] 1.2s Operating on slice 19 of 33: Fragment index slice generated in 1.47 s
  109. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 50745 spectra/s] 1.2s
  110. iPSC_7_phos_02.raw 32.8 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 51196 spectra/s] 1.2s
  111. iPSC_7_phos_03.raw 32.9 s | deisotoping 0.4 s [progress: 58689/58689 (100%) - 49277 spectra/s] 1.2s
  112. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 49976 spectra/s] 1.2s
  113. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 49889 spectra/s] 1.2s
  114. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 47325 spectra/s] 1.3s Operating on slice 20 of 33: Fragment index slice generated in 1.40 s
  115. iPSC_7_phos_01.raw 32.7 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 54056 spectra/s] 1.1s
  116. iPSC_7_phos_02.raw 32.7 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 47527 spectra/s] 1.2s
  117. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 50290 spectra/s] 1.2s
  118. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 50234 spectra/s] 1.2s
  119. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 54929 spectra/s] 1.1s
  120. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 47933 spectra/s] 1.2s Operating on slice 21 of 33: Fragment index slice generated in 1.40 s
  121. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 54256 spectra/s] 1.1s
  122. iPSC_7_phos_02.raw 32.7 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 54006 spectra/s] 1.1s
  123. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 50247 spectra/s] 1.2s
  124. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.3 s [progress: 58422/58422 (100%) - 53256 spectra/s] 1.1s
  125. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 51944 spectra/s] 1.1s
  126. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 52713 spectra/s] 1.1s Operating on slice 22 of 33: Fragment index slice generated in 1.39 s
  127. iPSC_7_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 52794 spectra/s] 1.1s
  128. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 50712 spectra/s] 1.2s
  129. iPSC_7_phos_03.raw 33.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 56001 spectra/s] 1.0s
  130. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 52491 spectra/s] 1.1s
  131. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 47339 spectra/s] 1.3s
  132. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 58899 spectra/s] 1.0s Operating on slice 23 of 33: Fragment index slice generated in 1.44 s
  133. iPSC_7_phos_01.raw 33.0 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 54965 spectra/s] 1.1s
  134. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 52846 spectra/s] 1.1s
  135. iPSC_7_phos_03.raw 33.2 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 54342 spectra/s] 1.1s
  136. iPSC_PT_phos_01.raw 32.7 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 52023 spectra/s] 1.1s
  137. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 53443 spectra/s] 1.1s
  138. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 52528 spectra/s] 1.1s Operating on slice 24 of 33: Fragment index slice generated in 1.39 s
  139. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 52278 spectra/s] 1.1s
  140. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 51916 spectra/s] 1.1s
  141. iPSC_7_phos_03.raw 33.2 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 57993 spectra/s] 1.0s
  142. iPSC_PT_phos_01.raw 33.0 s | deisotoping 0.3 s [progress: 58422/58422 (100%) - 56175 spectra/s] 1.0s
  143. iPSC_PT_phos_02.raw 33.6 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 56019 spectra/s] 1.1s
  144. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.4 s [progress: 59724/59724 (100%) - 58267 spectra/s] 1.0s Operating on slice 25 of 33: Fragment index slice generated in 1.39 s
  145. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 52700 spectra/s] 1.1s
  146. iPSC_7_phos_02.raw 33.0 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 51644 spectra/s] 1.1s
  147. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 55735 spectra/s] 1.1s
  148. iPSC_PT_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 51839 spectra/s] 1.1s
  149. iPSC_PT_phos_02.raw 33.5 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 47339 spectra/s] 1.3s
  150. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 59191 spectra/s] 1.0s Operating on slice 26 of 33: Fragment index slice generated in 1.45 s
  151. iPSC_7_phos_01.raw 32.7 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 52842 spectra/s] 1.1s
  152. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 51019 spectra/s] 1.2s
  153. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 56540 spectra/s] 1.0s
  154. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 52632 spectra/s] 1.1s
  155. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 53539 spectra/s] 1.1s
  156. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 51442 spectra/s] 1.2s Operating on slice 27 of 33: Fragment index slice generated in 1.38 s
  157. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 53032 spectra/s] 1.1s
  158. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 56813 spectra/s] 1.0s
  159. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 58339 spectra/s] 1.0s
  160. iPSC_PT_phos_01.raw 33.0 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 58016 spectra/s] 1.0s
  161. iPSC_PT_phos_02.raw 33.5 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 56770 spectra/s] 1.0s
  162. iPSC_PT_phos_03.raw 33.9 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 58097 spectra/s] 1.0s Operating on slice 28 of 33: Fragment index slice generated in 1.37 s
  163. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 57887 spectra/s] 1.0s
  164. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 52704 spectra/s] 1.1s
  165. iPSC_7_phos_03.raw 33.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 56432 spectra/s] 1.0s
  166. iPSC_PT_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 52116 spectra/s] 1.1s
  167. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 47188 spectra/s] 1.3s
  168. iPSC_PT_phos_03.raw 33.4 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 59191 spectra/s] 1.0s Operating on slice 29 of 33: Fragment index slice generated in 1.44 s
  169. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 52653 spectra/s] 1.1s
  170. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 52799 spectra/s] 1.1s
  171. iPSC_7_phos_03.raw 33.3 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 56704 spectra/s] 1.0s
  172. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.4 s [progress: 58422/58422 (100%) - 57786 spectra/s] 1.0s
  173. iPSC_PT_phos_02.raw 33.2 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 58739 spectra/s] 1.0s
  174. iPSC_PT_phos_03.raw 33.8 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 52115 spectra/s] 1.1s Operating on slice 30 of 33: Fragment index slice generated in 1.35 s
  175. iPSC_7_phos_01.raw 32.7 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 56715 spectra/s] 1.0s
  176. iPSC_7_phos_02.raw 33.1 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 57088 spectra/s] 1.0s
  177. iPSC_7_phos_03.raw 33.3 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 54442 spectra/s] 1.1s
  178. iPSC_PT_phos_01.raw 33.9 s | deisotoping 0.4 s [progress: 58422/58422 (100%) - 57844 spectra/s] 1.0s
  179. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 50613 spectra/s] 1.2s
  180. iPSC_PT_phos_03.raw 33.6 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 53135 spectra/s] 1.1s Operating on slice 31 of 33: Fragment index slice generated in 1.37 s
  181. iPSC_7_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 52700 spectra/s] 1.1s
  182. iPSC_7_phos_02.raw 32.8 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 56704 spectra/s] 1.0s
  183. iPSC_7_phos_03.raw 32.9 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 49030 spectra/s] 1.2s
  184. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 49510 spectra/s] 1.2s
  185. iPSC_PT_phos_02.raw 33.3 s | deisotoping 0.4 s [progress: 59268/59268 (100%) - 54176 spectra/s] 1.1s
  186. iPSC_PT_phos_03.raw 33.5 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 53468 spectra/s] 1.1s Operating on slice 32 of 33: Fragment index slice generated in 1.36 s
  187. iPSC_7_phos_01.raw 32.7 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 55747 spectra/s] 1.1s
  188. iPSC_7_phos_02.raw 32.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 48187 spectra/s] 1.2s
  189. iPSC_7_phos_03.raw 33.0 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 51572 spectra/s] 1.1s
  190. iPSC_PT_phos_01.raw 32.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 50320 spectra/s] 1.2s
  191. iPSC_PT_phos_02.raw 33.4 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 53588 spectra/s] 1.1s
  192. iPSC_PT_phos_03.raw 34.4 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 52528 spectra/s] 1.1s Operating on slice 33 of 33: Fragment index slice generated in 1.30 s
  193. iPSC_7_phos_01.raw 32.7 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 57491 spectra/s] 1.0s | postprocessing 0.9 s
  194. iPSC_7_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 56978 spectra/s] 1.0s | postprocessing 1.0 s
  195. iPSC_7_phos_03.raw 33.2 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 52730 spectra/s] 1.1s | postprocessing 1.1 s
  196. iPSC_PT_phos_01.raw 32.8 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 57164 spectra/s] 1.0s | postprocessing 1.0 s
  197. iPSC_PT_phos_02.raw 33.9 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 57598 spectra/s] 1.0s | postprocessing 0.9 s
  198. iPSC_PT_phos_03.raw 33.8 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 57207 spectra/s] 1.0s | postprocessing 1.0 s ***FIRST SEARCH DONE IN 139.745 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 -3.34 1.06 0.01 0.63 -3.94 2.89 -0.38 2.79
002 -3.16 1.05 -0.00 0.65 -3.71 2.92 -0.40 2.83
003 -3.23 1.03 0.01 0.63 -3.76 2.90 -0.31 2.82
004 -3.43 0.99 -0.02 0.64 -3.93 2.80 -0.37 2.72
005 -3.64 1.04 0.01 0.61 -4.11 2.84 -0.36 2.72
006 -3.54 1.02 -0.05 0.62 -3.96 2.85 -0.32 2.74
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 7 10 15 20 25 30
Count 24302 24680 24724 24698 skip rest
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- -------
Peaks 300_0 200_0 150_1 100_1
------- ------- ------- ------- -------
Count 25072 24983 skip rest
------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 25104
------- -------
------- -------
Rm P. 1
------- -------
Count 25139
------- -------

New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 23.927 MIN* ***TOTAL TIME 163.672 MIN**** STARTED: slice 1 of 3 ['C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx6G', WindowsPath('C:/MSFragger/MSFragger-3.1/MSFragger-3.1.jar'), 'fragger.params', WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_01.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_02.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_03.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_01.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_02.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_03.mzBIN_calibrated'), '--partial', '0'] Traceback (most recent call last): File "C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\msfragger_pep_split.py", line 470, in main() File "C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\msfragger_pep_split.py", line 459, in main run_msfragger(calibrate_mzBIN if calibrate_mass in [1, 2] else infiles_name) File "C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\tools\msfragger_pep_split.py", line 149, in run_msfragger subprocess.run(list(map(os.fspath, cmd)), cwd=cwd, check=True) File "C:\Users\User\anaconda3\lib\subprocess.py", line 512, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx6G', 'C:\MSFragger\MSFragger-3.1\MSFragger-3.1.jar', 'fragger.params', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_01.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_02.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_03.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_01.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_02.mzBIN_calibrated', 'D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_03.mzBIN_calibrated', '--partial', '0']' returned non-zero exit status 1. Process 'MsFragger' finished, exit code: 1 Process returned non-zero exit code, stoppingMsFragger move pepxml C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\jre\bin\java.exe -cp C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib\fragpipe-14.0.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_7_phos_01.pepXML D:\ADP-ribo\7_1\iPSC_7_phos_01.pepXML


Cancelling 58 remaining tasks
Processing interrupted, stopping MsFragger move pepxml
guoci commented 3 years ago

can you send the following files: fasta file fragger.params D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_01.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_02.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_03.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_01.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_02.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_03.mzBIN_calibrated

anesvi commented 3 years ago

You are searching ADP-ribo data, as it looks from the file name, feel free to contact us directly. MSFragger/FragPipe has a workflow for labile peptide identification, and we can help you with the settings. I am not sure the labile mode (which is part of the Glyco mode really) is well documented in our tutorials. But we can help, and it works great in our tests based on the publicly available Nielsen lab data. You can email me directly at nesvi at med.umich.edu

Best, Alexey

From: guoci notifications@github.com Sent: Wednesday, January 6, 2021 3:00 PM To: Nesvilab/FragPipe FragPipe@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: Re: [Nesvilab/FragPipe] Error as MsFragger' finished, exit code: 1 (#284)

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can you send the following files: fragger.params D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_01.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_02.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_03.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_01.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_02.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_03.mzBIN_calibrated

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Microbiomiao commented 3 years ago

Hi Guoci,

Attached please find the files you requested. However, I did not find any file of the file type of mzBIN_calibrated. Where can I find it? Thank you.

Best regards,

Miao-Hsia Lin, Ph.D. Assistant professor Department of Microbiology, College of Medicine, National Taiwan University E-mail: miaohsialin1012@ntu.edu.tw Tel:02-23123456 ext.88285

guoci notifications@github.com 於 2021年1月7日 週四 上午3:59寫道：

can you send the following files: fragger.params D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_01.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_02.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_7_phos_03.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_01.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_02.mzBIN_calibrated D:\ADP-ribo\split_peptide_index_tempdir\iPSC_PT_phos_03.mzBIN_calibrated

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guoci commented 3 years ago

There isn't any file attached. The mzBIN_calibrated are deleted by FragPipe. Please try a modified FragPipe to retain the files: https://drive.google.com/file/d/1JM-0TGPt6rZGOFrfzb1z0AXXx5jpDUzk/view?usp=sharing Also, can you rerun with more memory, you are currently using 6G only.

Microbiomiao commented 3 years ago

Dear Guoci,

I have run with new FragPipe and the error is still there. Attached please find the log and parameter files. I used memory as 10G this time. Thanks for your help.

Best regards, Miao-Hsia Lin, Ph.D. Assistant professor Department of Microbiology, College of Medicine, National Taiwan University E-mail: miaohsialin1012@ntu.edu.tw Tel:02-23123456 ext.88285

guoci notifications@github.com 於 2021年1月12日 週二 上午2:27寫道：

There isn't any file attached. The mzBIN_calibrated are deleted by FragPipe. Please try a modified FragPipe to retain the files:

https://drive.google.com/file/d/1JM-0TGPt6rZGOFrfzb1z0AXXx5jpDUzk/view?usp=sharing Also, can you rerun with more memory, you are currently using 6G only.

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System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 14.1-build13 MSFragger version 3.1.1 Philosopher version 3.3.12 (build 1604525264)

LCMS files: Experiment/Group: 7_1

69 commands to execute: WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck MSFragger [Work dir: D:\ADP-ribo] C:\Users\User\anaconda3\pythonw.exe C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\msfragger_pep_split.py 2 "C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx10G" C:\MSFragger\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\ADP-ribo\fragger.params D:\ADP-ribo\iPSC_7_phos_01.raw D:\ADP-ribo\iPSC_7_phos_02.raw D:\ADP-ribo\iPSC_7_phos_03.raw D:\ADP-ribo\iPSC_PT_phos_01.raw D:\ADP-ribo\iPSC_PT_phos_02.raw D:\ADP-ribo\iPSC_PT_phos_03.raw MSFragger move pepxml C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_7_phos_01.pepXML D:\ADP-ribo\7_1\iPSC_7_phos_01.pepXML MSFragger move tsv C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove --no-err D:\ADP-ribo\iPSC_7_phos_01.tsv D:\ADP-ribo\7_1\iPSC_7_phos_01.tsv MSFragger move pepxml C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_7_phos_02.pepXML D:\ADP-ribo\7_2\iPSC_7_phos_02.pepXML MSFragger move tsv C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove --no-err D:\ADP-ribo\iPSC_7_phos_02.tsv D:\ADP-ribo\7_2\iPSC_7_phos_02.tsv MSFragger move pepxml C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_7_phos_03.pepXML D:\ADP-ribo\7_3\iPSC_7_phos_03.pepXML MSFragger move tsv C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove --no-err D:\ADP-ribo\iPSC_7_phos_03.tsv D:\ADP-ribo\7_3\iPSC_7_phos_03.tsv MSFragger move pepxml C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_PT_phos_01.pepXML D:\ADP-ribo\PT_1\iPSC_PT_phos_01.pepXML MSFragger move tsv C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove --no-err D:\ADP-ribo\iPSC_PT_phos_01.tsv D:\ADP-ribo\PT_1\iPSC_PT_phos_01.tsv MSFragger move pepxml C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_PT_phos_02.pepXML D:\ADP-ribo\PT_2\iPSC_PT_phos_02.pepXML MSFragger move tsv C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove --no-err D:\ADP-ribo\iPSC_PT_phos_02.tsv D:\ADP-ribo\PT_2\iPSC_PT_phos_02.tsv MSFragger move pepxml C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove D:\ADP-ribo\iPSC_PT_phos_03.pepXML D:\ADP-ribo\PT_3\iPSC_PT_phos_03.pepXML MSFragger move tsv C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib\fragpipe-14.1-build13.jar com.github.chhh.utils.FileMove --no-err D:\ADP-ribo\iPSC_PT_phos_03.tsv D:\ADP-ribo\PT_3\iPSC_PT_phos_03.tsv PeptideProphet [Work dir: D:\ADP-ribo\PT2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas --combine iPSC_PT_phos_02.pepXML PeptideProphet [Work dir: D:\ADP-ribo\PT1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas --combine iPSC_PT_phos_01.pepXML PeptideProphet [Work dir: D:\ADP-ribo\71] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas --combine iPSC_7_phos_01.pepXML PeptideProphet [Work dir: D:\ADP-ribo\72] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas --combine iPSC_7_phos_02.pepXML PeptideProphet [Work dir: D:\ADP-ribo\73] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas --combine iPSC_7_phos_03.pepXML PeptideProphet [Work dir: D:\ADP-ribo\PT3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe peptideprophet --nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2 --decoy rev --database C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas --combine iPSC_PT_phos_03.pepXML Rewrite pepxml [Work dir: D:\ADP-ribo\PT_3] C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\PT_3\interact.pep.xml D:\ADP-ribo\iPSC_PT_phos_03.raw Rewrite pepxml [Work dir: D:\ADP-ribo\7_2] C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\7_2\interact.pep.xml D:\ADP-ribo\iPSC_7_phos_02.raw Rewrite pepxml [Work dir: D:\ADP-ribo\PT_2] C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\PT_2\interact.pep.xml D:\ADP-ribo\iPSC_PT_phos_02.raw Rewrite pepxml [Work dir: D:\ADP-ribo\PT_1] C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\PT_1\interact.pep.xml D:\ADP-ribo\iPSC_PT_phos_01.raw Rewrite pepxml [Work dir: D:\ADP-ribo\7_3] C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\7_3\interact.pep.xml D:\ADP-ribo\iPSC_7_phos_03.raw Rewrite pepxml [Work dir: D:\ADP-ribo\7_1] C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -cp C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\lib/ com.dmtavt.fragpipe.util.RewritePepxml D:\ADP-ribo\7_1\interact.pep.xml D:\ADP-ribo\iPSC_7_phos_01.raw ProteinProphet [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined D:\ADP-ribo\7_3\interact.pep.xml D:\ADP-ribo\PT_1\interact.pep.xml D:\ADP-ribo\PT_3\interact.pep.xml D:\ADP-ribo\7_1\interact.pep.xml D:\ADP-ribo\7_2\interact.pep.xml D:\ADP-ribo\PT_2\interact.pep.xml PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe database --annotate C:\MaxQuant\2020-12-29-decoys-uniprot_homosapiens_reviewed20201029.fasta.fas --prefix rev PhilosopherFilter [Work dir: D:\ADP-ribo\72] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml D:\ADP-ribo\7_2 --protxml D:\ADP-ribo\combined.prot.xml PhilosopherFilter [Work dir: D:\ADP-ribo\PT2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml D:\ADP-ribo\PT_2 --protxml D:\ADP-ribo\combined.prot.xml PhilosopherFilter [Work dir: D:\ADP-ribo\PT1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml D:\ADP-ribo\PT_1 --protxml D:\ADP-ribo\combined.prot.xml PhilosopherFilter [Work dir: D:\ADP-ribo\PT3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml D:\ADP-ribo\PT_3 --protxml D:\ADP-ribo\combined.prot.xml PhilosopherFilter [Work dir: D:\ADP-ribo\71] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml D:\ADP-ribo\7_1 --protxml D:\ADP-ribo\combined.prot.xml PhilosopherFilter [Work dir: D:\ADP-ribo\73] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe filter --sequential --razor --mapmods --prot 0.01 --tag rev --pepxml D:\ADP-ribo\7_3 --protxml D:\ADP-ribo\combined.prot.xml PhilosopherReport [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherReport [Work dir: D:\ADP-ribo\PT3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe report PhilosopherAbacus [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe abacus --razor --reprint --tag rev --protein 7_2 PT_2 PT_1 PT_3 7_1 7_3 IonQuant [Work dir: D:\ADP-ribo] C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -Xmx10G -Dlibs.bruker.dir="C:\MSFragger\MSFragger-3.1.1\ext\bruker" -Dlibs.thermo.dir="C:\MSFragger\MSFragger-3.1.1\ext\thermo" -cp "C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\ionquant-1.5.2.jar;C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\batmass-io-1.22.1.jar" ionquant.IonQuant --threads 15 --ionmobility 0 --mbr 1 --proteinquant 2 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 3 --minfreq 0.5 --minions 2 --minexps 1 --psm 7_2\psm.tsv --psm PT_2\psm.tsv --psm PT_1\psm.tsv --psm PT_3\psm.tsv --psm 7_1\psm.tsv --psm 7_3\psm.tsv --multidir . --specdir D:\ADP-ribo 7_3\iPSC_7_phos_03.pepXML PT_1\iPSC_PT_phos_01.pepXML PT_3\iPSC_PT_phos_03.pepXML 7_1\iPSC_7_phos_01.pepXML 7_2\iPSC_7_phos_02.pepXML PT_2\iPSC_PT_phos_02.pepXML WorkspaceClean [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck PTMShepherd [Work dir: D:\ADP-ribo] C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -Xmx10G -Dbatmass.io.libs.thermo.dir="C:\MSFragger\MSFragger-3.1.1\ext\thermo" -cp "C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\ptmshepherd-0.4.0.jar;C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\batmass-io-1.22.1.jar;C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\commons-math3-3.6.1.jar" edu.umich.andykong.ptmshepherd.PTMShepherd "D:\ADP-ribo\shepherd.config"


Execution order:

    Cmd: [START], Work dir: [D:\ADP-ribo]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\7_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\7_3]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\PT_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\PT_2]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\7_1]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo]
    Cmd: [WorkspaceCleanInit], Work dir: [D:\ADP-ribo\PT_3]
    Cmd: [MSFragger], Work dir: [D:\ADP-ribo]
    Cmd: [PeptideProphet], Work dir: [D:\ADP-ribo]
    Cmd: [ProteinProphet], Work dir: [D:\ADP-ribo]
    Cmd: [PhilosopherDbAnnotate], Work dir: [D:\ADP-ribo]
    Cmd: [PhilosopherFilter], Work dir: [D:\ADP-ribo]
    Cmd: [PhilosopherReport], Work dir: [D:\ADP-ribo]
    Cmd: [PhilosopherAbacus], Work dir: [D:\ADP-ribo]
    Cmd: [IonQuant], Work dir: [D:\ADP-ribo]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\7_2]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\7_3]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\PT_1]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\PT_2]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\7_1]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo]
    Cmd: [WorkspaceClean], Work dir: [D:\ADP-ribo\PT_3]
    Cmd: [PTMShepherd], Work dir: [D:\ADP-ribo]

# FragPipe v14.1-build13ui state cache

crystalc.run-crystalc=false
database.db-path=C\:\\MaxQuant\\2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas
database.decoy-tag=rev_
fragpipe-config.bin-msfragger=C\:\\MSFragger\\MSFragger-3.1.1\\MSFragger-3.1.1.jar
fragpipe-config.bin-philosopher=C\:\\Users\\User\\Downloads\\FragPipe-jre-14.0\\fragpipe\\lib\\..\\tools\\philosopher\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\User\\anaconda3\\pythonw.exe
freequant.mz-tol=10
freequant.rt-tol=0.4
freequant.run-freequant=false
ionquant.excludemods=
ionquant.heavy=
ionquant.imtol=0.05
ionquant.ionfdr=0.01
ionquant.light=
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minexps=1
ionquant.minfreq=0.5
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.proteinquant=2
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=3
ionquant.writeindex=0
msfragger.Y_type_masses=0 114.03169 193.99802 291.97492 406.00661
msfragger.add_topN_complementary=0
msfragger.allow_multiple_variable_mods_on_residue=false
msfragger.allowed_missed_cleavage=3
msfragger.calibrate_mass=2
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.diagnostic_fragments=136.06232 250.09401 348.07036 428.03669 584.09018
msfragger.diagnostic_intensity_filter=0.03
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y,Y
msfragger.fragment_mass_tolerance=0.1
msfragger.fragment_mass_units=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=labile
msfragger.localize_delta_mass=true
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0 541.06111
msfragger.max_fragment_charge=1
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=trypsin
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=2
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=corrected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remove_precursor_peak=0
msfragger.report_alternative_proteins=false
msfragger.restrict_deltamass_to=STYKRE
msfragger.run-msfragger=true
msfragger.search_enzyme_butnotafter=P
msfragger.search_enzyme_cutafter=KR
msfragger.search_enzyme_name=trypsin
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; 57.021460,C (cysteine),true,-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,true,2; -17.026500,nQnC,false,1; -18.010600,nE,false,1; 0.000000,site_06,false,1; 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_topN_peaks=150
msfragger.write_calibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
peptide-prophet.cmd-opts=--nonparam --expectscore --decoyprobs --masswidth 1000.0 --clevel -2
peptide-prophet.combine-pepxml=true
peptide-prophet.run-peptide-prophet=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --razor --mapmods --prot 0.01
phi-report.pep-level-summary=false
phi-report.print-decoys=false
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.annotation-common=true
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-unimod=false
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.diag_ions=
ptmshepherd.glyco_mode=false
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_background=4
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=1
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=3
ptmshepherd.precursor_mass_units=1
ptmshepherd.precursor_tol=3
ptmshepherd.remainder_masses=
ptmshepherd.run-shepherd=true
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.varmod_masses=Failed_Carbamidomethylation\:-57.021464
quantitation.run-label-free-quant=true
speclibgen.easypqp.extras.rt_lowess_fraction=0.01
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.run-speclibgen=false
speclibgen.use-easypqp=false
speclibgen.use-spectrast=true
tmtintegrator.add_Ref=1
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=false
tmtintegrator.best_psm=true
tmtintegrator.channel_num=4
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=0.9
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=1
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=D\:\\ADP-ribo
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.process-exps-separately=false
workflow.ram=10
workflow.threads=15

WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:59:49] Executing Workspace v3.3.12
INFO[14:59:49] Removing workspace
WARN[14:59:49] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:59:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:59:49] Executing Workspace v3.3.12
INFO[14:59:49] Creating workspace
INFO[14:59:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:59:49] Executing Workspace v3.3.12
INFO[14:59:50] Removing workspace
WARN[14:59:50] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:59:50] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[14:59:50] Executing Workspace v3.3.12
INFO[14:59:50] Creating workspace
INFO[14:59:50] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[14:59:50] Executing Workspace v3.3.12
INFO[14:59:50] Removing workspace
WARN[14:59:50] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:59:50] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:59:50] Executing Workspace v3.3.12
INFO[14:59:50] Creating workspace
INFO[14:59:50] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:59:50] Executing Workspace v3.3.12
INFO[14:59:50] Removing workspace
WARN[14:59:50] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:59:50] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_2] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:59:50] Executing Workspace v3.3.12
INFO[14:59:51] Creating workspace
INFO[14:59:51] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck INFO[14:59:51] Executing Workspace v3.3.12
INFO[14:59:51] Removing workspace
WARN[14:59:51] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:59:51] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo\7_1] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck INFO[14:59:51] Executing Workspace v3.3.12
INFO[14:59:51] Creating workspace
INFO[14:59:51] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[14:59:51] Executing Workspace v3.3.12
INFO[14:59:51] Removing workspace
INFO[14:59:51] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[14:59:52] Executing Workspace v3.3.12
INFO[14:59:52] Creating workspace
INFO[14:59:52] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --clean --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[14:59:53] Executing Workspace v3.3.12
INFO[14:59:53] Removing workspace
WARN[14:59:53] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[14:59:53] Done
WorkspaceCleanInit [Work dir: D:\ADP-ribo\PT_3] C:\Users\User\Downloads\FragPipe-jre-14.0\fragpipe\lib..\tools\philosopher\philosopher.exe workspace --init --nocheck Process 'WorkspaceCleanInit' finished, exit code: 0 INFO[14:59:53] Executing Workspace v3.3.12
INFO[14:59:53] Creating workspace
INFO[14:59:53] Done
MSFragger [Work dir: D:\ADP-ribo] C:\Users\User\anaconda3\pythonw.exe C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\msfragger_pep_split.py 2 "C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx10G" C:\MSFragger\MSFragger-3.1.1\MSFragger-3.1.1.jar D:\ADP-ribo\fragger.params D:\ADP-ribo\iPSC_7_phos_01.raw D:\ADP-ribo\iPSC_7_phos_02.raw D:\ADP-ribo\iPSC_7_phos_03.raw D:\ADP-ribo\iPSC_PT_phos_01.raw D:\ADP-ribo\iPSC_PT_phos_02.raw D:\ADP-ribo\iPSC_PT_phos_03.raw ['C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx10G', WindowsPath('C:/MSFragger/MSFragger-3.1.1/MSFragger-3.1.1.jar'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/fragger.params'), '--split1', WindowsPath('D:/ADP-ribo/iPSC_7_phos_01.raw'), WindowsPath('D:/ADP-ribo/iPSC_7_phos_02.raw'), WindowsPath('D:/ADP-ribo/iPSC_7_phos_03.raw'), WindowsPath('D:/ADP-ribo/iPSC_PT_phos_01.raw'), WindowsPath('D:/ADP-ribo/iPSC_PT_phos_02.raw'), WindowsPath('D:/ADP-ribo/iPSC_PT_phos_03.raw')] MSFragger version MSFragger-3.1.1 Batmass-IO version 1.19.5 timsdata library version timsdata-2-7-0 (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: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 10 GB memory Checking database... Checking D:\ADP-ribo\iPSC_7_phos_01.raw... Checking D:\ADP-ribo\iPSC_7_phos_02.raw... Checking D:\ADP-ribo\iPSC_7_phos_03.raw... Checking D:\ADP-ribo\iPSC_PT_phos_01.raw... Checking D:\ADP-ribo\iPSC_PT_phos_02.raw... Checking D:\ADP-ribo\iPSC_PT_phos_03.raw... ***FIRST SEARCH**** Parameters: num_threads = 15 database_name = 2020-12-29-decoys-uniprot_homosapiens_reviewed_20201029.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 100.0 fragment_mass_units = 1 calibrate_mass = 2 write_calibrated_mgf = false isotope_error = 0/1 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = CORRECTED 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_cutafter = KR search_enzyme_butnotafter = P num_enzyme_termini = 2 allowed_missed_cleavage = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_file_extension = pepXML output_format = pepXML output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = false override_charge = false precursor_charge_low = 1 precursor_charge_high = 4 digest_min_length = 7 digest_max_length = 50 digest_mass_range_low = 500.0 digest_mass_range_high = 5000.0 max_fragment_charge = 1 deisotope = 1 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 = 150 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 variable_mod_01 = 15.994900 M 3 variable_mod_02 = 42.010600 [^ 1 variable_mod_03 = 79.966330 STY 2 add_A_alanine = 0.000000 add_B_user_amino_acid = 0.000000 add_C_cysteine = 57.021460 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 (255.15829 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 7: 292531 of length 8: 283762 of length 9: 279636 of length 10: 268063 of length 11: 256973 of length 12: 245870 of length 13: 241189 of length 14: 225703 of length 15: 217529 of length 16: 204247 of length 17: 192417 of length 18: 186591 of length 19: 181284 of length 20: 166186 of length 21: 159445 of length 22: 150833 of length 23: 141055 of length 24: 135378 of length 25: 127583 of length 26: 119850 of length 27: 114682 of length 28: 111852 of length 29: 101445 of length 30: 96253 of length 31: 90482 of length 32: 86323 of length 33: 81434 of length 34: 75407 of length 35: 70034 of length 36: 68237 of length 37: 62489 of length 38: 58709 of length 39: 53747 of length 40: 51136 of length 41: 48053 of length 42: 43565 of length 43: 37750 of length 44: 30176 of length 45: 22785 of length 46: 15056 of length 47: 9051 of length 48: 5165 of length 49: 2654 of length 50: 1471 In total 5414081 peptides. Generated 97699051 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.50 Da. 5580783570 fragments to be searched in 14 slices (83.16 GB total) Operating on slice 1 of 14: Fragment index slice generated in 6.34 s

  1. iPSC_7_phos_01.raw 49.6 s | deisotoping 1.2 s [progress: 58813/58813 (100%) - 8229 spectra/s] 7.1s
  2. iPSC_7_phos_02.raw 34.2 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 9625 spectra/s] 6.1s
  3. iPSC_7_phos_03.raw 34.1 s | deisotoping 0.3 s [progress: 58689/58689 (100%) - 12286 spectra/s] 4.8s
  4. iPSC_PT_phos_01.raw 35.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 11333 spectra/s] 5.2s
  5. iPSC_PT_phos_02.raw 34.7 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 12276 spectra/s] 4.8s
  6. iPSC_PT_phos_03.raw 35.2 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 10500 spectra/s] 5.7s Operating on slice 2 of 14: Fragment index slice generated in 5.45 s
  7. iPSC_7_phos_01.raw 33.6 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 17431 spectra/s] 3.4s
  8. iPSC_7_phos_02.raw 33.4 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 16370 spectra/s] 3.6s
  9. iPSC_7_phos_03.raw 34.5 s | deisotoping 0.3 s [progress: 58689/58689 (100%) - 16574 spectra/s] 3.5s
  10. iPSC_PT_phos_01.raw 33.8 s | deisotoping 0.3 s [progress: 58422/58422 (100%) - 17138 spectra/s] 3.4s
  11. iPSC_PT_phos_02.raw 34.6 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 15342 spectra/s] 3.9s
  12. iPSC_PT_phos_03.raw 34.5 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 13787 spectra/s] 4.3s Operating on slice 3 of 14: Fragment index slice generated in 5.02 s
  13. iPSC_7_phos_01.raw 34.7 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 23601 spectra/s] 2.5s
  14. iPSC_7_phos_02.raw 34.2 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 24443 spectra/s] 2.4s
  15. iPSC_7_phos_03.raw 33.5 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 24393 spectra/s] 2.4s
  16. iPSC_PT_phos_01.raw 34.6 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 24332 spectra/s] 2.4s
  17. iPSC_PT_phos_02.raw 34.2 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 22822 spectra/s] 2.6s
  18. iPSC_PT_phos_03.raw 34.2 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 24792 spectra/s] 2.4s Operating on slice 4 of 14: Fragment index slice generated in 4.17 s
  19. iPSC_7_phos_01.raw 34.6 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 28262 spectra/s] 2.1s
  20. iPSC_7_phos_02.raw 33.7 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 28434 spectra/s] 2.1s
  21. iPSC_7_phos_03.raw 35.3 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 24282 spectra/s] 2.4s
  22. iPSC_PT_phos_01.raw 35.3 s | deisotoping 0.3 s [progress: 58422/58422 (100%) - 25368 spectra/s] 2.3s
  23. iPSC_PT_phos_02.raw 36.4 s | deisotoping 0.3 s [progress: 59268/59268 (100%) - 25995 spectra/s] 2.3s
  24. iPSC_PT_phos_03.raw 35.5 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 23634 spectra/s] 2.5s Operating on slice 5 of 14: Fragment index slice generated in 4.69 s
  25. iPSC_7_phos_01.raw 33.3 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 29333 spectra/s] 2.0s
  26. iPSC_7_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 29783 spectra/s] 2.0s
  27. iPSC_7_phos_03.raw 33.2 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 29746 spectra/s] 2.0s
  28. iPSC_PT_phos_01.raw 33.3 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 29551 spectra/s] 2.0s
  29. iPSC_PT_phos_02.raw 33.7 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 25927 spectra/s] 2.3s
  30. iPSC_PT_phos_03.raw 35.8 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 22063 spectra/s] 2.7s Operating on slice 6 of 14: Fragment index slice generated in 4.75 s
  31. iPSC_7_phos_01.raw 33.6 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 33550 spectra/s] 1.8s
  32. iPSC_7_phos_02.raw 34.9 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 29828 spectra/s] 2.0s
  33. iPSC_7_phos_03.raw 33.7 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 32659 spectra/s] 1.8s
  34. iPSC_PT_phos_01.raw 33.4 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 33868 spectra/s] 1.7s
  35. iPSC_PT_phos_02.raw 34.4 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 32405 spectra/s] 1.8s
  36. iPSC_PT_phos_03.raw 34.9 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 34109 spectra/s] 1.8s Operating on slice 7 of 14: Fragment index slice generated in 4.69 s
  37. iPSC_7_phos_01.raw 33.6 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 41979 spectra/s] 1.4s
  38. iPSC_7_phos_02.raw 34.4 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 44753 spectra/s] 1.3s
  39. iPSC_7_phos_03.raw 33.3 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 39468 spectra/s] 1.5s
  40. iPSC_PT_phos_01.raw 33.3 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 41641 spectra/s] 1.4s
  41. iPSC_PT_phos_02.raw 34.1 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 40931 spectra/s] 1.4s
  42. iPSC_PT_phos_03.raw 35.1 s | deisotoping 0.3 s [progress: 59724/59724 (100%) - 40795 spectra/s] 1.5s Operating on slice 8 of 14: Fragment index slice generated in 4.77 s
  43. iPSC_7_phos_01.raw 34.0 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 41535 spectra/s] 1.4s
  44. iPSC_7_phos_02.raw 33.3 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 40156 spectra/s] 1.5s
  45. iPSC_7_phos_03.raw 33.4 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 43506 spectra/s] 1.3s
  46. iPSC_PT_phos_01.raw 33.4 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 39608 spectra/s] 1.5s
  47. iPSC_PT_phos_02.raw 34.5 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 32872 spectra/s] 1.8s
  48. iPSC_PT_phos_03.raw 35.8 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 40823 spectra/s] 1.5s Operating on slice 9 of 14: Fragment index slice generated in 4.77 s
  49. iPSC_7_phos_01.raw 35.2 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 39314 spectra/s] 1.5s
  50. iPSC_7_phos_02.raw 33.8 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 38059 spectra/s] 1.6s
  51. iPSC_7_phos_03.raw 35.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 29974 spectra/s] 2.0s
  52. iPSC_PT_phos_01.raw 35.6 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 29521 spectra/s] 2.0s
  53. iPSC_PT_phos_02.raw 35.5 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 38763 spectra/s] 1.5s
  54. iPSC_PT_phos_03.raw 35.5 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 39138 spectra/s] 1.5s Operating on slice 10 of 14: Fragment index slice generated in 4.93 s
  55. iPSC_7_phos_01.raw 34.6 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 34718 spectra/s] 1.7s
  56. iPSC_7_phos_02.raw 35.2 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 40710 spectra/s] 1.5s
  57. iPSC_7_phos_03.raw 34.6 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 38560 spectra/s] 1.5s
  58. iPSC_PT_phos_01.raw 34.6 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 40236 spectra/s] 1.5s
  59. iPSC_PT_phos_02.raw 35.4 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 39355 spectra/s] 1.5s
  60. iPSC_PT_phos_03.raw 35.5 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 32283 spectra/s] 1.9s Operating on slice 11 of 14: Fragment index slice generated in 4.59 s
  61. iPSC_7_phos_01.raw 34.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 40145 spectra/s] 1.5s
  62. iPSC_7_phos_02.raw 34.6 s | deisotoping 0.3 s [progress: 59029/59029 (100%) - 43628 spectra/s] 1.4s
  63. iPSC_7_phos_03.raw 34.3 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 39601 spectra/s] 1.5s
  64. iPSC_PT_phos_01.raw 34.9 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 34549 spectra/s] 1.7s
  65. iPSC_PT_phos_02.raw 34.0 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 41738 spectra/s] 1.4s
  66. iPSC_PT_phos_03.raw 34.1 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 40573 spectra/s] 1.5s Operating on slice 12 of 14: Fragment index slice generated in 4.10 s
  67. iPSC_7_phos_01.raw 33.5 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 43023 spectra/s] 1.4s
  68. iPSC_7_phos_02.raw 33.4 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 42589 spectra/s] 1.4s
  69. iPSC_7_phos_03.raw 34.3 s | deisotoping 0.3 s [progress: 58689/58689 (100%) - 36006 spectra/s] 1.6s
  70. iPSC_PT_phos_01.raw 35.3 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 40402 spectra/s] 1.4s
  71. iPSC_PT_phos_02.raw 35.1 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 42700 spectra/s] 1.4s
  72. iPSC_PT_phos_03.raw 35.9 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 41246 spectra/s] 1.4s Operating on slice 13 of 14: Fragment index slice generated in 4.24 s
  73. iPSC_7_phos_01.raw 35.1 s | deisotoping 0.3 s [progress: 58813/58813 (100%) - 35927 spectra/s] 1.6s
  74. iPSC_7_phos_02.raw 34.8 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 43372 spectra/s] 1.4s
  75. iPSC_7_phos_03.raw 34.0 s | deisotoping 0.3 s [progress: 58689/58689 (100%) - 38611 spectra/s] 1.5s
  76. iPSC_PT_phos_01.raw 35.6 s | deisotoping 0.2 s [progress: 58422/58422 (100%) - 36491 spectra/s] 1.6s
  77. iPSC_PT_phos_02.raw 36.3 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 46303 spectra/s] 1.3s
  78. iPSC_PT_phos_03.raw 34.4 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 43562 spectra/s] 1.4s Operating on slice 14 of 14: Fragment index slice generated in 3.63 s
  79. iPSC_7_phos_01.raw 33.8 s | deisotoping 0.2 s [progress: 58813/58813 (100%) - 46975 spectra/s] 1.3s | postprocessing 1.3 s
  80. iPSC_7_phos_02.raw 35.3 s | deisotoping 0.2 s [progress: 59029/59029 (100%) - 46480 spectra/s] 1.3s | postprocessing 0.8 s
  81. iPSC_7_phos_03.raw 35.1 s | deisotoping 0.2 s [progress: 58689/58689 (100%) - 44529 spectra/s] 1.3s | postprocessing 0.6 s
  82. iPSC_PT_phos_01.raw 35.7 s | deisotoping 0.3 s [progress: 58422/58422 (100%) - 36085 spectra/s] 1.6s | postprocessing 0.5 s
  83. iPSC_PT_phos_02.raw 34.0 s | deisotoping 0.2 s [progress: 59268/59268 (100%) - 47490 spectra/s] 1.2s | postprocessing 0.5 s
  84. iPSC_PT_phos_03.raw 34.6 s | deisotoping 0.2 s [progress: 59724/59724 (100%) - 47513 spectra/s] 1.3s | postprocessing 0.5 s ***FIRST SEARCH DONE IN 54.481 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 -3.34 1.05 0.03 0.62 -3.94 2.89 -0.36 2.82
002 -3.13 1.07 0.02 0.63 -3.73 2.92 -0.42 2.81
003 -3.25 1.04 -0.01 0.61 -3.76 2.90 -0.29 2.85
004 -3.44 1.00 -0.02 0.63 -3.92 2.81 -0.30 2.68
005 -3.63 1.05 0.01 0.60 -4.07 2.80 -0.25 2.70
006 -3.55 1.04 -0.05 0.63 -3.96 2.83 -0.30 2.73
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- MS2 7 10 15 20 25 30
Count 24103 24578 24611 24567 skip rest
------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- -------
Peaks 300_0 200_0 150_1 100_1
------- ------- ------- ------- -------
Count 24973 24880 24611 skip rest
------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 24920
------- -------
------- -------
Rm P. 1
------- -------
Count 24923
------- -------

New fragment_mass_tolerance = 15 PPM New use_topN_peaks = 200 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 1 New precursor_true_tolerance = 4.000000 PPM (tie breaker) ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 22.312 MIN* ***TOTAL TIME 76.792 MIN**** STARTED: slice 1 of 2 ['C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx10G', WindowsPath('C:/MSFragger/MSFragger-3.1.1/MSFragger-3.1.1.jar'), 'fragger.params', WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_01.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_02.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_03.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_01.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_02.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_03.mzBIN_calibrated'), '--partial', '0'] DONE: slice 1 of 2 STARTED: slice 2 of 2 ['C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx10G', WindowsPath('C:/MSFragger/MSFragger-3.1.1/MSFragger-3.1.1.jar'), 'fragger.params', WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_01.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_02.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_7_phos_03.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_01.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_02.mzBIN_calibrated'), WindowsPath('D:/ADP-ribo/split_peptide_index_tempdir/iPSC_PT_phos_03.mzBIN_calibrated'), '--partial', '1'] DONE: slice 2 of 2 ['C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\jre\bin\java.exe', '-jar', '-Dfile.encoding=UTF-8', '-Xmx10G', WindowsPath('C:/MSFragger/MSFragger-3.1.1/MSFragger-3.1.1.jar'), '--generate_expect_functions', 'iPSC_7_phos_01_scores_histogram.tsv', 'iPSC_7_phos_02_scores_histogram.tsv', 'iPSC_7_phos_03_scores_histogram.tsv', 'iPSC_PT_phos_01_scores_histogram.tsv', 'iPSC_PT_phos_02_scores_histogram.tsv', 'iPSC_PT_phos_03_scores_histogram.tsv'] Traceback (most recent call last): File "C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\msfragger_pep_split.py", line 480, in main() File "C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\msfragger_pep_split.py", line 475, in main combine_results() File "C:\MSFragger\FragPipe-jre-14.1-build13\fragpipe\tools\msfragger_pep_split.py", line 336, in combine_results e.result() File "C:\Users\User\anaconda3\lib\concurrent\futures_base.py", line 432, in result return self.get_result() File "C:\Users\User\anaconda3\lib\concurrent\futures_base.py", line 388, in get_result raise self._exception concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending. Process 'MSFragger' finished, exit code: 1 Process returned non-zero exit code, stopping


Cancelling 55 remaining tasks
fcyu commented 3 years ago

@guoci Is there any update?

Thanks,

Fengchao

guoci commented 3 years ago

@fcyu I am still waiting for the files. Please see my earlier comment

fcyu commented 3 years ago

It's been a while, if @Microbiomiao hasn't sent you the file in a few days, I think we can close this issue.

Best,

Fengchao

Microbiomiao commented 3 years ago

Hi Guoci, Dan helps me out and it works well now. Thank you for your help. You can close this issue. Thanks again. Best regards,

Miao-Hsia Lin, Ph.D. Assistant professor Department of Microbiology, College of Medicine, National Taiwan University E-mail: miaohsialin1012@ntu.edu.tw Tel:02-23123456 ext.88285

guoci notifications@github.com 於 2021年1月12日 週二 上午2:27寫道：

There isn't any file attached. The mzBIN_calibrated are deleted by FragPipe. Please try a modified FragPipe to retain the files:

https://drive.google.com/file/d/1JM-0TGPt6rZGOFrfzb1z0AXXx5jpDUzk/view?usp=sharing Also, can you rerun with more memory, you are currently using 6G only.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/284#issuecomment-758138013, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASJ6TGXRSZYCTUTO4VQGZ4DSZM7J5ANCNFSM4VUA4LFQ .