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Nesvilab / FragPipe

A cross-platform Graphical User Interface (GUI) for running MSFragger and Philosopher - powered pipeline for comprehensive analysis of shotgun proteomics data
http://fragpipe.nesvilab.org
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MSBooster error code 132 on virtual machine #989

Closed Tlicknack closed 1 year ago

Tlicknack commented 1 year ago

I'll attach the log from the failed run below, and I can upload the successful run if you think that will be helpful.

Thank you.

Version info: FragPipe version 19.1 MSFragger version 3.7 IonQuant version 1.8.10 Philosopher version 4.8.1

LCMS files: Experiment/Group: wolM_1

81 commands to execute: CheckCentroid java -Xmx114G -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/tools/batmass-io-1.28.9.jar com.dmtavt.fragpipe.util.CheckCentroid /home/tlicknac/fragpipe_test/DmWOL-Sperm2.raw 6 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4d0bf60d-85ee-47e2-a0a0-e01cf8aeb71f WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/1f5d677e-f1fe-41c9-861b-9aac25ed01c2 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4a92a8d2-edb9-4ffb-a901-76446116e704 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/cc0d98a6-81f8-4d03-b8f2-a7294ec8bff6 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4606e779-6b57-45b6-914c-0f47692fb7f7 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/327a1360-9f79-4ab4-a7ad-832a46b091f8 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/e9158a9b-94d7-48ef-9ca4-6960045d8a97 MSFragger [Work dir: /home/tlicknac/fragpipe_test/FP-out] java -jar -Dfile.encoding=UTF-8 -Xmx114G /home/tlicknac/software/fragpipe/tools/MSFragger-3.7/MSFragger-3.7.jar /home/tlicknac/fragpipe_test/FP-out/fragger.params /home/tlicknac/fragpipe_test/DmWOL-Sperm2.raw /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722084851.raw /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722133447.raw /home/tlicknac/fragpipe_test/DmWOL+Sperm1.raw /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721183103.raw /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721231700.raw MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2.pepXML /home/tlicknac/fragpipe_test/FP-out/wolM_1/DmWOL-Sperm2.pepXML MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2.pin /home/tlicknac/fragpipe_test/FP-out/wolM_1/DmWOL-Sperm2.pin MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722084851.pepXML /home/tlicknac/fragpipe_test/FP-out/wolM_2/DmWOL-Sperm2_20210722084851.pepXML MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722084851.pin /home/tlicknac/fragpipe_test/FP-out/wolM_2/DmWOL-Sperm2_20210722084851.pin MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722133447.pepXML /home/tlicknac/fragpipe_test/FP-out/wolM_3/DmWOL-Sperm2_20210722133447.pepXML MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722133447.pin /home/tlicknac/fragpipe_test/FP-out/wolM_3/DmWOL-Sperm2_20210722133447.pin MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1.pepXML /home/tlicknac/fragpipe_test/FP-out/wolP_1/DmWOL+Sperm1.pepXML MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1.pin /home/tlicknac/fragpipe_test/FP-out/wolP_1/DmWOL+Sperm1.pin MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721183103.pepXML /home/tlicknac/fragpipe_test/FP-out/wolP_2/DmWOL+Sperm1_20210721183103.pepXML MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721183103.pin /home/tlicknac/fragpipe_test/FP-out/wolP_2/DmWOL+Sperm1_20210721183103.pin MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721231700.pepXML /home/tlicknac/fragpipe_test/FP-out/wolP_3/DmWOL+Sperm1_20210721231700.pepXML MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721231700.pin /home/tlicknac/fragpipe_test/FP-out/wolP_3/DmWOL+Sperm1_20210721231700.pin MSBooster [Work dir: /home/tlicknac/fragpipe_test/FP-out] java -Xmx114G -cp /home/tlicknac/software/fragpipe/tools/msbooster-1.1.11.jar:/home/tlicknac/software/fragpipe/tools/batmass-io-1.28.9.jar Features.MainClass --paramsList /home/tlicknac/fragpipe_test/FP-out/msbooster_params.txt Percolator [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] /home/tlicknac/software/fragpipe/tools/percolator-305/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 6 --results-psms DmWOL+Sperm1_20210721183103_percolator_target_psms.tsv --decoy-results-psms DmWOL+Sperm1_20210721183103_percolator_decoy_psms.tsv DmWOL+Sperm1_20210721183103_edited.pin Percolator [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] /home/tlicknac/software/fragpipe/tools/percolator-305/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 6 --results-psms DmWOL+Sperm1_20210721231700_percolator_target_psms.tsv --decoy-results-psms DmWOL+Sperm1_20210721231700_percolator_decoy_psms.tsv DmWOL+Sperm1_20210721231700_edited.pin Percolator [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] /home/tlicknac/software/fragpipe/tools/percolator-305/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 6 --results-psms DmWOL+Sperm1_percolator_target_psms.tsv --decoy-results-psms DmWOL+Sperm1_percolator_decoy_psms.tsv DmWOL+Sperm1_edited.pin Percolator [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] /home/tlicknac/software/fragpipe/tools/percolator-305/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 6 --results-psms DmWOL-Sperm2_percolator_target_psms.tsv --decoy-results-psms DmWOL-Sperm2_percolator_decoy_psms.tsv DmWOL-Sperm2_edited.pin Percolator [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] /home/tlicknac/software/fragpipe/tools/percolator-305/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 6 --results-psms DmWOL-Sperm2_20210722084851_percolator_target_psms.tsv --decoy-results-psms DmWOL-Sperm2_20210722084851_percolator_decoy_psms.tsv DmWOL-Sperm2_20210722084851_edited.pin Percolator [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] /home/tlicknac/software/fragpipe/tools/percolator-305/percolator --only-psms --no-terminate --post-processing-tdc --num-threads 6 --results-psms DmWOL-Sperm2_20210722133447_percolator_target_psms.tsv --decoy-results-psms DmWOL-Sperm2_20210722133447_percolator_decoy_psms.tsv DmWOL-Sperm2_20210722133447_edited.pin Percolator: Convert to pepxml [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] java -cp /home/tlicknac/software/fragpipe/lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML DmWOL+Sperm1_20210721183103.pin DmWOL+Sperm1_20210721183103 DmWOL+Sperm1_20210721183103_percolator_target_psms.tsv DmWOL+Sperm1_20210721183103_percolator_decoy_psms.tsv interact-DmWOL+Sperm1_20210721183103 DDA 0.5 Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolP_2/DmWOL+Sperm1_20210721183103_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolP_2/DmWOL+Sperm1_20210721183103_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] java -cp /home/tlicknac/software/fragpipe/lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML DmWOL+Sperm1_20210721231700.pin DmWOL+Sperm1_20210721231700 DmWOL+Sperm1_20210721231700_percolator_target_psms.tsv DmWOL+Sperm1_20210721231700_percolator_decoy_psms.tsv interact-DmWOL+Sperm1_20210721231700 DDA 0.5 Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolP_3/DmWOL+Sperm1_20210721231700_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolP_3/DmWOL+Sperm1_20210721231700_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] java -cp /home/tlicknac/software/fragpipe/lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML DmWOL+Sperm1.pin DmWOL+Sperm1 DmWOL+Sperm1_percolator_target_psms.tsv DmWOL+Sperm1_percolator_decoy_psms.tsv interact-DmWOL+Sperm1 DDA 0.5 Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolP_1/DmWOL+Sperm1_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolP_1/DmWOL+Sperm1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] java -cp /home/tlicknac/software/fragpipe/lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML DmWOL-Sperm2.pin DmWOL-Sperm2 DmWOL-Sperm2_percolator_target_psms.tsv DmWOL-Sperm2_percolator_decoy_psms.tsv interact-DmWOL-Sperm2 DDA 0.5 Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolM_1/DmWOL-Sperm2_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolM_1/DmWOL-Sperm2_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] java -cp /home/tlicknac/software/fragpipe/lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML DmWOL-Sperm2_20210722084851.pin DmWOL-Sperm2_20210722084851 DmWOL-Sperm2_20210722084851_percolator_target_psms.tsv DmWOL-Sperm2_20210722084851_percolator_decoy_psms.tsv interact-DmWOL-Sperm2_20210722084851 DDA 0.5 Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolM_2/DmWOL-Sperm2_20210722084851_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolM_2/DmWOL-Sperm2_20210722084851_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] java -cp /home/tlicknac/software/fragpipe/lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML DmWOL-Sperm2_20210722133447.pin DmWOL-Sperm2_20210722133447 DmWOL-Sperm2_20210722133447_percolator_target_psms.tsv DmWOL-Sperm2_20210722133447_percolator_decoy_psms.tsv interact-DmWOL-Sperm2_20210722133447 DDA 0.5 Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolM_3/DmWOL-Sperm2_20210722133447_percolator_target_psms.tsv Percolator: Delete temp java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar com.github.chhh.utils.FileDelete /home/tlicknac/fragpipe_test/FP-out/wolM_3/DmWOL-Sperm2_20210722133447_percolator_decoy_psms.tsv ProteinProphet [Work dir: /home/tlicknac/fragpipe_test/FP-out] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher proteinprophet --maxppmdiff 2000000 --output combined /home/tlicknac/fragpipe_test/FP-out/filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher database --annotate /home/tlicknac/fragpipetest/2023-01-19-decoys-contam-dmel-proteome.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher database --annotate /home/tlicknac/fragpipetest/2023-01-19-decoys-contam-dmel-proteome.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher database --annotate /home/tlicknac/fragpipetest/2023-01-19-decoys-contam-dmel-proteome.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher database --annotate /home/tlicknac/fragpipetest/2023-01-19-decoys-contam-dmel-proteome.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher database --annotate /home/tlicknac/fragpipetest/2023-01-19-decoys-contam-dmel-proteome.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher database --annotate /home/tlicknac/fragpipetest/2023-01-19-decoys-contam-dmel-proteome.fasta.fas --prefix rev PhilosopherDbAnnotate [Work dir: /home/tlicknac/fragpipe_test/FP-out] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher database --annotate /home/tlicknac/fragpipetest/2023-01-19-decoys-contam-dmel-proteome.fasta.fas --prefix rev PhilosopherFilter [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linuxamd64/philosopher filter --sequential --prot 0.01 --tag rev --pepxml /home/tlicknac/fragpipe_test/FP-out/wolM_1 --protxml /home/tlicknac/fragpipe_test/FP-out/combined.prot.xml --razor PhilosopherFilter [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linuxamd64/philosopher filter --sequential --prot 0.01 --tag rev --pepxml /home/tlicknac/fragpipe_test/FP-out/wolM_2 --protxml /home/tlicknac/fragpipe_test/FP-out/combined.prot.xml --razorbin /home/tlicknac/fragpipe_test/FP-out/wolM_1/.meta/razor.bin PhilosopherFilter [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linuxamd64/philosopher filter --sequential --prot 0.01 --tag rev --pepxml /home/tlicknac/fragpipe_test/FP-out/wolM_3 --protxml /home/tlicknac/fragpipe_test/FP-out/combined.prot.xml --razorbin /home/tlicknac/fragpipe_test/FP-out/wolM_1/.meta/razor.bin PhilosopherFilter [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linuxamd64/philosopher filter --sequential --prot 0.01 --tag rev --pepxml /home/tlicknac/fragpipe_test/FP-out/wolP_1 --protxml /home/tlicknac/fragpipe_test/FP-out/combined.prot.xml --razorbin /home/tlicknac/fragpipe_test/FP-out/wolM_1/.meta/razor.bin PhilosopherFilter [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linuxamd64/philosopher filter --sequential --prot 0.01 --tag rev --pepxml /home/tlicknac/fragpipe_test/FP-out/wolP_2 --protxml /home/tlicknac/fragpipe_test/FP-out/combined.prot.xml --razorbin /home/tlicknac/fragpipe_test/FP-out/wolM_1/.meta/razor.bin PhilosopherFilter [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linuxamd64/philosopher filter --sequential --prot 0.01 --tag rev --pepxml /home/tlicknac/fragpipe_test/FP-out/wolP_3 --protxml /home/tlicknac/fragpipe_test/FP-out/combined.prot.xml --razorbin /home/tlicknac/fragpipe_test/FP-out/wolM_1/.meta/razor.bin PhilosopherReport [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher report PhilosopherReport [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher report WorkspaceClean [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck WorkspaceClean [Work dir: /home/tlicknac/fragpipe_test/FP-out] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck IonQuant [Work dir: /home/tlicknac/fragpipe_test/FP-out] java -Xmx114G -Dlibs.bruker.dir=/home/tlicknac/software/fragpipe/tools/MSFragger-3.7/ext/bruker -Dlibs.thermo.dir=/home/tlicknac/software/fragpipe/tools/MSFragger-3.7/ext/thermo -cp /home/tlicknac/software/fragpipe/tools/jfreechart-1.5.3.jar:/home/tlicknac/software/fragpipe/tools/batmass-io-1.28.9.jar:/home/tlicknac/software/fragpipe/tools/IonQuant-1.8.10.jar ionquant.IonQuant --threads 6 --ionmobility 0 --minexps 1 --mbr 1 --maxlfq 0 --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 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist /home/tlicknac/fragpipe_test/FP-out/filelist_ionquant.txt --modlist /home/tlicknac/fragpipe_test/FP-out/modmasses_ionquant.txt


Execution order:

    Cmd: [START], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [CheckCentroid], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [WorkspaceCleanInit], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolP_2]
    Cmd: [WorkspaceCleanInit], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolP_3]
    Cmd: [WorkspaceCleanInit], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolM_3]
    Cmd: [WorkspaceCleanInit], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolP_1]
    Cmd: [WorkspaceCleanInit], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolM_1]
    Cmd: [WorkspaceCleanInit], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolM_2]
    Cmd: [WorkspaceCleanInit], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [MSFragger], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [MSBooster], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [Percolator], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [ProteinProphet], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [PhilosopherDbAnnotate], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [PhilosopherFilter], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [PhilosopherReport], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [WorkspaceClean], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolP_2]
    Cmd: [WorkspaceClean], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolP_3]
    Cmd: [WorkspaceClean], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolM_3]
    Cmd: [WorkspaceClean], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolP_1]
    Cmd: [WorkspaceClean], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolM_1]
    Cmd: [WorkspaceClean], Work dir: [/home/tlicknac/fragpipe_test/FP-out/wolM_2]
    Cmd: [WorkspaceClean], Work dir: [/home/tlicknac/fragpipe_test/FP-out]
    Cmd: [IonQuant], Work dir: [/home/tlicknac/fragpipe_test/FP-out]

>rev_sp|A0A0B4K692|NEP2_DROME Neprilysin-2 OS=Drosophila melanogaster OX=7227 GN=Nep2 PE=1 SV=1
>rev_sp|Q9V3J4|SEC13_DROME Protein SEC13 homolog OS=Drosophila melanogaster OX=7227 GN=Sec13 PE=1 SV=1
>rev_tr|A0A0B4KEE9|A0A0B4KEE9_DROME Optix, isoform C OS=Drosophila melanogaster OX=7227 GN=Optix PE=4 SV=1
>rev_tr|A1Z8W1|A1Z8W1_DROME Salto, isoform A OS=Drosophila melanogaster OX=7227 GN=salto PE=4 SV=1
>rev_tr|E8NH35|E8NH35_DROME Complexin, isoform Z OS=Drosophila melanogaster OX=7227 GN=cpx PE=1 SV=1
>rev_tr|M9PI73|M9PI73_DROME RING-type E3 ubiquitin transferase OS=Drosophila melanogaster OX=7227 GN=mib1 PE=4 SV=1
>rev_tr|Q86BG6|Q86BG6_DROME AT02269p OS=Drosophila melanogaster OX=7227 GN=Dmel\CG10508 PE=2 SV=3
>rev_tr|Q9VA99|Q9VA99_DROME Sod_Cu domain-containing protein OS=Drosophila melanogaster OX=7227 GN=Dmel\CG31028 PE=4 SV=5
>rev_tr|Q9VLJ4|Q9VLJ4_DROME FI04485p OS=Drosophila melanogaster OX=7227 GN=Dmel\CG17834 PE=2 SV=2
>rev_tr|Q9VXV2|Q9VXV2_DROME MIP04191p OS=Drosophila melanogaster OX=7227 GN=Dmel\CG6294 PE=2 SV=1
>rev_tr|X2JLD3|X2JLD3_DROME RPA_C domain-containing protein OS=Drosophila melanogaster OX=7227 GN=Dmel\CG45491 PE=4 SV=1
>sp|Q9V3H2|PSDE_DROME 26S proteasome non-ATPase regulatory subunit 14 OS=Drosophila melanogaster OX=7227 GN=Rpn11 PE=1 SV=1
>tr|A0A0B4KED8|A0A0B4KED8_DROME Patched-related, isoform D OS=Drosophila melanogaster OX=7227 GN=Ptr PE=4 SV=1
>tr|A1Z8V5|A1Z8V5_DROME Dynein regulatory complex protein 10 OS=Drosophila melanogaster OX=7227 GN=Dmel\CG13168 PE=3 SV=1
>tr|E6EK17|E6EK17_DROME Calcium-transporting ATPase OS=Drosophila melanogaster OX=7227 GN=PMCA PE=1 SV=1
>tr|M9PI59|M9PI59_DROME Shade, isoform D OS=Drosophila melanogaster OX=7227 GN=shd PE=3 SV=1
>tr|Q86BB5|Q86BB5_DROME Transforming acidic coiled-coil protein, isoform D OS=Drosophila melanogaster OX=7227 GN=tacc PE=1 SV=1
>tr|Q9VA92|Q9VA92_DROME RH14937p OS=Drosophila melanogaster OX=7227 GN=anon-WO0118547.264 PE=2 SV=2
>tr|Q9VLI4|Q9VLI4_DROME Raw, isoform A OS=Drosophila melanogaster OX=7227 GN=raw PE=4 SV=2
>tr|Q9VXU6|Q9VXU6_DROME Protein with SprT-like domain at the N terminus OS=Drosophila melanogaster OX=7227 GN=mh PE=1 SV=1
>tr|X2JL49|X2JL49_DROME Ubiquitin carboxyl-terminal hydrolase MINDY OS=Drosophila melanogaster OX=7227 GN=Dmel\CG7332 PE=3 SV=1
# FragPipe v19.1ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=/home/tlicknac/fragpipe_test/2023-01-19-decoys-contam-dmel-proteome.fasta.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=true
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fragpipe-config.bin-ionquant=/home/tlicknac/software/fragpipe/tools/IonQuant-1.8.10.jar
fragpipe-config.bin-msfragger=/home/tlicknac/software/fragpipe/tools/MSFragger-3.7/MSFragger-3.7.jar
fragpipe-config.bin-philosopher=/home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher
fragpipe-config.bin-python=/home/tlicknac/.conda/envs/FRAGPIPE_CONDA/bin/python
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.locprob=0.75
ionquant.maxlfq=0
ionquant.mbr=1
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=2
ionquant.minisotopes=2
ionquant.minscans=3
ionquant.mztol=10
ionquant.normalization=1
ionquant.peptidefdr=1
ionquant.proteinfdr=1
ionquant.requantify=1
ionquant.rttol=0.4
ionquant.run-ionquant=true
ionquant.tp=0
ionquant.uniqueness=0
ionquant.use-labeling=false
ionquant.use-lfq=true
ionquant.writeindex=0
msbooster.predict-rt=true
msbooster.predict-spectra=true
msbooster.run-msbooster=true
msbooster.use-correlated-features=false
msfragger.Y_type_masses=
msfragger.activation_types=all
msfragger.add_topN_complementary=0
msfragger.allowed_missed_cleavage_1=2
msfragger.allowed_missed_cleavage_2=2
msfragger.calibrate_mass=2
msfragger.check_spectral_files=true
msfragger.clip_nTerm_M=true
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
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=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name_1=stricttrypsin
msfragger.search_enzyme_name_2=null
msfragger.search_enzyme_nocut_1=
msfragger.search_enzyme_nocut_2=
msfragger.search_enzyme_sense_1=C
msfragger.search_enzyme_sense_2=C
msfragger.table.fix-mods=0.0,C-Term Peptide,true,-1; 0.0,N-Term Peptide,true,-1; 0.0,C-Term Protein,true,-1; 0.0,N-Term Protein,true,-1; 0.0,G (glycine),true,-1; 0.0,A (alanine),true,-1; 0.0,S (serine),true,-1; 0.0,P (proline),true,-1; 0.0,V (valine),true,-1; 0.0,T (threonine),true,-1; 57.02146,C (cysteine),true,-1; 0.0,L (leucine),true,-1; 0.0,I (isoleucine),true,-1; 0.0,N (asparagine),true,-1; 0.0,D (aspartic acid),true,-1; 0.0,Q (glutamine),true,-1; 0.0,K (lysine),true,-1; 0.0,E (glutamic acid),true,-1; 0.0,M (methionine),true,-1; 0.0,H (histidine),true,-1; 0.0,F (phenylalanine),true,-1; 0.0,R (arginine),true,-1; 0.0,Y (tyrosine),true,-1; 0.0,W (tryptophan),true,-1; 0.0,B ,true,-1; 0.0,J,true,-1; 0.0,O,true,-1; 0.0,U,true,-1; 0.0,X,true,-1; 0.0,Z,true,-1
msfragger.table.var-mods=15.9949,M,true,3; 42.0106,[^,true,1; 79.96633,STY,false,3; -17.0265,nQnC,false,1; -18.0106,nE,false,1; 4.025107,K,false,2; 6.020129,R,false,2; 8.014199,K,false,2; 10.008269,R,false,2; 0.0,site_10,false,1; 0.0,site_11,false,1; 0.0,site_12,false,1; 0.0,site_13,false,1; 0.0,site_14,false,1; 0.0,site_15,false,1; 0.0,site_16,false,1
msfragger.track_zero_topN=0
msfragger.use_all_mods_in_first_search=false
msfragger.use_topN_peaks=150
msfragger.write_calibrated_mzml=false
msfragger.write_uncalibrated_mgf=false
msfragger.zero_bin_accept_expect=0
msfragger.zero_bin_mult_expect=1
opair.activation1=HCD
opair.activation2=ETD
opair.glyco_db=
opair.max_glycans=4
opair.max_isotope_error=2
opair.min_isotope_error=0
opair.ms1_tol=20
opair.ms2_tol=20
opair.reverse_scan_order=false
opair.run-opair=false
opair.single_scan_type=false
peptide-prophet.cmd-opts=--decoyprobs --ppm --accmass --nonparam --expectscore
peptide-prophet.combine-pepxml=false
peptide-prophet.run-peptide-prophet=false
percolator.cmd-opts=--only-psms --no-terminate --post-processing-tdc
percolator.keep-tsv-files=false
percolator.min-prob=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --prot 0.01
phi-report.pep-level-summary=true
phi-report.philosoher-msstats=true
phi-report.print-decoys=false
phi-report.prot-level-summary=true
phi-report.remove-contaminants=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 STY\:79.966331,M\:15.9949 MINPROB\=0.5
ptmprophet.run-ptmprophet=false
ptmshepherd.adv_params=false
ptmshepherd.annotation-common=false
ptmshepherd.annotation-custom=false
ptmshepherd.annotation-glyco=false
ptmshepherd.annotation-unimod=true
ptmshepherd.annotation_file=
ptmshepherd.annotation_tol=0.01
ptmshepherd.cap_y_ions=
ptmshepherd.decoy_type=1
ptmshepherd.diag_ions=
ptmshepherd.diagextract_mode=false
ptmshepherd.diagmine_diagMinFoldChange=3.0
ptmshepherd.diagmine_diagMinSpecDiff=00.2
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=00.1
ptmshepherd.diagmine_fragMinSpecDiff=00.1
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=00.2
ptmshepherd.glyco_adducts=
ptmshepherd.glyco_fdr=1.00
ptmshepherd.glyco_isotope_max=3
ptmshepherd.glyco_isotope_min=-1
ptmshepherd.glyco_mode=false
ptmshepherd.glyco_ppm_tol=50
ptmshepherd.glycodatabase=
ptmshepherd.histo_smoothbins=2
ptmshepherd.iontype_a=false
ptmshepherd.iontype_b=true
ptmshepherd.iontype_c=false
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=false
ptmshepherd.localization_allowed_res=
ptmshepherd.localization_background=4
ptmshepherd.max_adducts=0
ptmshepherd.n_glyco=true
ptmshepherd.normalization-psms=true
ptmshepherd.normalization-scans=false
ptmshepherd.output_extended=false
ptmshepherd.peakpicking_mass_units=0
ptmshepherd.peakpicking_minPsm=10
ptmshepherd.peakpicking_promRatio=0.3
ptmshepherd.peakpicking_width=0.002
ptmshepherd.precursor_mass_units=0
ptmshepherd.precursor_tol=0.01
ptmshepherd.print_decoys=false
ptmshepherd.prob_dhexOx=2,0.5,0.1
ptmshepherd.prob_dhexY=2,0.5
ptmshepherd.prob_neuacOx=2,0.05,0.2
ptmshepherd.prob_neugcOx=2,0.05,0.2
ptmshepherd.prob_phosphoOx=2,0.05,0.2
ptmshepherd.prob_regY=5,0.5
ptmshepherd.prob_sulfoOx=2,0.05,0.2
ptmshepherd.remainder_masses=
ptmshepherd.remove_glycan_delta_mass=true
ptmshepherd.run-shepherd=false
ptmshepherd.spectra_maxfragcharge=2
ptmshepherd.spectra_ppmtol=20
ptmshepherd.varmod_masses=
quantitation.run-label-free-quant=true
run-psm-validation=true
run-validation-tab=true
saintexpress.fragpipe.cmd-opts=
saintexpress.max-replicates=10
saintexpress.run-saint-express=false
saintexpress.virtual-controls=100
speclibgen.easypqp.extras.max_delta_ppm=15
speclibgen.easypqp.extras.max_delta_unimod=0.02
speclibgen.easypqp.extras.rt_lowess_fraction=0
speclibgen.easypqp.fragment.a=false
speclibgen.easypqp.fragment.b=true
speclibgen.easypqp.fragment.c=false
speclibgen.easypqp.fragment.x=false
speclibgen.easypqp.fragment.y=true
speclibgen.easypqp.fragment.z=false
speclibgen.easypqp.im-cal=Automatic selection of a run as reference IM
speclibgen.easypqp.neutral_loss=false
speclibgen.easypqp.rt-cal=noiRT
speclibgen.easypqp.select-file.text=
speclibgen.easypqp.select-im-file.text=
speclibgen.keep-intermediate-files=false
speclibgen.run-speclibgen=false
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tmtintegrator.add_Ref=-1
tmtintegrator.aggregation_method=0
tmtintegrator.allow_overlabel=true
tmtintegrator.allow_unlabeled=true
tmtintegrator.best_psm=true
tmtintegrator.channel_num=TMT-6
tmtintegrator.dont-run-fq-lq=false
tmtintegrator.glyco_qval=-1
tmtintegrator.groupby=0
tmtintegrator.log2transformed=true
tmtintegrator.max_pep_prob_thres=0
tmtintegrator.min_ntt=0
tmtintegrator.min_pep_prob=0.9
tmtintegrator.min_percent=0.05
tmtintegrator.min_purity=0.5
tmtintegrator.min_site_prob=-1
tmtintegrator.mod_tag=none
tmtintegrator.ms1_int=true
tmtintegrator.outlier_removal=true
tmtintegrator.print_RefInt=false
tmtintegrator.prot_exclude=none
tmtintegrator.prot_norm=0
tmtintegrator.psm_norm=false
tmtintegrator.quant_level=2
tmtintegrator.ref_tag=Bridge
tmtintegrator.run-tmtintegrator=false
tmtintegrator.tolerance=20
tmtintegrator.top3_pep=true
tmtintegrator.unique_gene=0
tmtintegrator.unique_pep=false
tmtintegrator.use_glycan_composition=false
workdir=/home/tlicknac/fragpipe_test/FP-out
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=6

CheckCentroid java -Xmx114G -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/tools/batmass-io-1.28.9.jar com.dmtavt.fragpipe.util.CheckCentroid /home/tlicknac/fragpipe_test/DmWOL-Sperm2.raw 6 Done in 0 ms. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck time="09:00:00" level=info msg="Executing Workspace v4.8.1" time="09:00:00" level=info msg="Removing workspace" time="09:00:00" level=warning msg="Cannot read file. open .meta/meta.bin: no such file or directory" time="09:00:00" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4d0bf60d-85ee-47e2-a0a0-e01cf8aeb71f time="09:00:00" level=info msg="Executing Workspace v4.8.1" time="09:00:00" level=info msg="Creating workspace" time="09:00:00" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck time="09:00:00" level=info msg="Executing Workspace v4.8.1" time="09:00:00" level=info msg="Removing workspace" time="09:00:00" level=warning msg="Cannot read file. open .meta/meta.bin: no such file or directory" time="09:00:00" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/1f5d677e-f1fe-41c9-861b-9aac25ed01c2 time="09:00:00" level=info msg="Executing Workspace v4.8.1" time="09:00:00" level=info msg="Creating workspace" time="09:00:01" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck time="09:00:01" level=info msg="Executing Workspace v4.8.1" time="09:00:01" level=info msg="Removing workspace" time="09:00:01" level=warning msg="Cannot read file. open .meta/meta.bin: no such file or directory" time="09:00:01" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_3] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4a92a8d2-edb9-4ffb-a901-76446116e704 time="09:00:01" level=info msg="Executing Workspace v4.8.1" time="09:00:01" level=info msg="Creating workspace" time="09:00:01" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck time="09:00:01" level=info msg="Executing Workspace v4.8.1" time="09:00:01" level=info msg="Removing workspace" time="09:00:01" level=warning msg="Cannot read file. open .meta/meta.bin: no such file or directory" time="09:00:01" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolP_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/cc0d98a6-81f8-4d03-b8f2-a7294ec8bff6 time="09:00:01" level=info msg="Executing Workspace v4.8.1" time="09:00:01" level=info msg="Creating workspace" time="09:00:01" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck time="09:00:02" level=info msg="Executing Workspace v4.8.1" time="09:00:02" level=info msg="Removing workspace" time="09:00:02" level=warning msg="Cannot read file. open .meta/meta.bin: no such file or directory" time="09:00:02" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_1] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/4606e779-6b57-45b6-914c-0f47692fb7f7 time="09:00:02" level=info msg="Executing Workspace v4.8.1" time="09:00:02" level=info msg="Creating workspace" time="09:00:02" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck time="09:00:02" level=info msg="Executing Workspace v4.8.1" time="09:00:02" level=info msg="Removing workspace" time="09:00:02" level=warning msg="Cannot read file. open .meta/meta.bin: no such file or directory" time="09:00:02" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out/wolM_2] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/327a1360-9f79-4ab4-a7ad-832a46b091f8 time="09:00:02" level=info msg="Executing Workspace v4.8.1" time="09:00:02" level=info msg="Creating workspace" time="09:00:02" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --clean --nocheck time="09:00:02" level=info msg="Executing Workspace v4.8.1" time="09:00:02" level=info msg="Removing workspace" time="09:00:02" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: /home/tlicknac/fragpipe_test/FP-out] /home/tlicknac/software/fragpipe/tools/philosopher_v4.8.1_linux_amd64/philosopher workspace --init --nocheck --temp /tmp/e9158a9b-94d7-48ef-9ca4-6960045d8a97 time="09:00:03" level=info msg="Executing Workspace v4.8.1" time="09:00:03" level=info msg="Creating workspace" time="09:00:03" level=info msg=Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: /home/tlicknac/fragpipe_test/FP-out] java -jar -Dfile.encoding=UTF-8 -Xmx114G /home/tlicknac/software/fragpipe/tools/MSFragger-3.7/MSFragger-3.7.jar /home/tlicknac/fragpipe_test/FP-out/fragger.params /home/tlicknac/fragpipe_test/DmWOL-Sperm2.raw /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722084851.raw /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722133447.raw /home/tlicknac/fragpipe_test/DmWOL+Sperm1.raw /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721183103.raw /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721231700.raw MSFragger version MSFragger-3.7 Batmass-IO version 1.28.9 timsdata library version timsdata-2-21-0-4 (c) University of Michigan RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. timdTOF .d reading tool. Copyright (c) 2022 by Bruker Daltonics GmbH & Co. KG. All rights reserved. System OS: Linux, Architecture: amd64 Java Info: 12.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation JVM started with 114 GB memory Checking database... Checking spectral files... /home/tlicknac/fragpipe_test/DmWOL+Sperm1.raw: Scans = 75329 /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721183103.raw: Scans = 76519 /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721231700.raw: Scans = 77687 /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722133447.raw: Scans = 121159 /home/tlicknac/fragpipe_test/DmWOL-Sperm2.raw: Scans = 118227 /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722084851.raw: Scans = 118298 The data appears to be low resolution MS/MS. Switching to 300 ppm fragment tolerance. ***FIRST SEARCH**** Parameters: num_threads = 6 database_name = /home/tlicknac/fragpipe_test/2023-01-19-decoys-contam-dmel-proteome.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 300.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mzml = 0 write_uncalibrated_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 = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin 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 = 0 deneutralloss = false 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 activation_types = all remove_precursor_peak = 1 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 204893 of length 8: 197601 of length 9: 187400 of length 10: 179008 of length 11: 171463 of length 12: 162329 of length 13: 153920 of length 14: 146587 of length 15: 139076 of length 16: 131528 of length 17: 123425 of length 18: 118291 of length 19: 111522 of length 20: 105445 of length 21: 100163 of length 22: 93131 of length 23: 88152 of length 24: 84126 of length 25: 78464 of length 26: 73723 of length 27: 69165 of length 28: 65669 of length 29: 60806 of length 30: 58449 of length 31: 54745 of length 32: 50602 of length 33: 47647 of length 34: 44708 of length 35: 41391 of length 36: 38898 of length 37: 36670 of length 38: 33928 of length 39: 31625 of length 40: 29424 of length 41: 27003 of length 42: 24774 of length 43: 21262 of length 44: 17067 of length 45: 12528 of length 46: 8265 of length 47: 5228 of length 48: 3358 of length 49: 1906 of length 50: 1224 In total 3436589 peptides. Generated 5723091 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 1.50 Da. 237499630 fragments to be searched in 1 slices (3.54 GB total) Operating on slice 1 of 1: Fragment index slice generated in 4.62 s

  1. DmWOL+Sperm1.raw 52.0 s [progress: 75329/75329 (100%) - 6777 spectra/s] 11.1s | postprocessing 0.8 s
  2. DmWOL+Sperm1_20210721183103.raw 43.7 s [progress: 76519/76519 (100%) - 8547 spectra/s] 9.0s | postprocessing 0.5 s
  3. DmWOL+Sperm1_20210721231700.raw 41.7 s [progress: 77687/77687 (100%) - 8957 spectra/s] 8.7s | postprocessing 0.5 s
  4. DmWOL-Sperm2.raw 63.5 s [progress: 118227/118227 (100%) - 7820 spectra/s] 15.1s | postprocessing 0.6 s
  5. DmWOL-Sperm2_20210722084851.raw 60.0 s [progress: 118298/118298 (100%) - 8042 spectra/s] 14.7s | postprocessing 0.5 s
  6. DmWOL-Sperm2_20210722133447.raw 63.0 s [progress: 121157/121157 (100%) - 8094 spectra/s] 15.0s | postprocessing 0.6 s ***FIRST SEARCH DONE IN 7.615 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 -6.00 0.69 -0.06 0.51 120.76 95.43 22.17 100.71
002 -5.89 0.65 0.01 0.45 121.77 95.35 24.01 101.55
003 -6.05 0.67 -0.06 0.51 125.24 94.19 25.93 98.76
004 -5.76 0.65 -0.05 0.49 126.96 92.17 23.63 95.47
005 -6.05 0.69 -0.06 0.51 129.04 90.92 23.44 94.97
006 -5.90 0.74 -0.17 0.59 126.88 91.99 24.34 94.12
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 150 200 250 300 350 400 450 500
Count skip skip 2989 1251 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- -------
Peaks 150_1 125_1 100_1 75_1
------- ------- ------- ------- -------
Count 2989 4465 3992 skip rest
------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 2281
------- -------
------- -------
Rm P. 0
------- -------
Count 4494
------- -------
------- -------
FragChg 1
------- -------
Count 6767
------- -------

New fragment_mass_tolerance = 250 PPM New use_topN_peaks = 125 New minimum_ratio = 0.010000 New intensity_transform = 0 New remove_precursor_peak = 0 New max_fragment_charge = 1 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 7.643 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 6 database_name = /home/tlicknac/fragpipe_test/2023-01-19-decoys-contam-dmel-proteome.fasta.fas decoyprefix = rev precursor_mass_lower = -20.0 precursor_mass_upper = 20.0 precursor_mass_units = 1 data_type = 0 precursor_true_tolerance = 20.0 precursor_true_units = 1 fragment_mass_tolerance = 250.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = false write_calibrated_mzml = 0 write_uncalibrated_mgf = false isotope_error = 0/1/2 mass_offsets = 0.0 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 = stricttrypsin search_enzyme_sense_1 = C search_enzyme_cut_1 = KR search_enzyme_nocut_1 = allowed_missed_cleavage_1 = 2 num_enzyme_termini = 2 clip_nTerm_M = true allow_multiple_variable_mods_on_residue = false max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 50.0 report_alternative_proteins = true 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 = 0 deneutralloss = false 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 = 125 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = true variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 add_A_alanine = 0.0 add_B_user_amino_acid = 0.0 add_C_cysteine = 57.02146 add_Cterm_peptide = 0.0 add_Cterm_protein = 0.0 add_D_aspartic_acid = 0.0 add_E_glutamic_acid = 0.0 add_F_phenylalanine = 0.0 add_G_glycine = 0.0 add_H_histidine = 0.0 add_I_isoleucine = 0.0 add_J_user_amino_acid = 0.0 add_K_lysine = 0.0 add_L_leucine = 0.0 add_M_methionine = 0.0 add_N_asparagine = 0.0 add_Nterm_peptide = 0.0 add_Nterm_protein = 0.0 add_O_user_amino_acid = 0.0 # O = pyrrolysine (237.14773 Da) add_P_proline = 0.0 add_Q_glutamine = 0.0 add_R_arginine = 0.0 add_S_serine = 0.0 add_T_threonine = 0.0 add_U_user_amino_acid = 0.0 # U = selenocysteine (150.95363 Da) add_V_valine = 0.0 add_W_tryptophan = 0.0 add_X_user_amino_acid = 0.0 add_Y_tyrosine = 0.0 add_Z_user_amino_acid = 0.0 Number of unique peptides of length 7: 204893 of length 8: 197601 of length 9: 187400 of length 10: 179008 of length 11: 171463 of length 12: 162329 of length 13: 153920 of length 14: 146587 of length 15: 139076 of length 16: 131528 of length 17: 123425 of length 18: 118291 of length 19: 111522 of length 20: 105445 of length 21: 100163 of length 22: 93131 of length 23: 88152 of length 24: 84126 of length 25: 78464 of length 26: 73723 of length 27: 69165 of length 28: 65669 of length 29: 60806 of length 30: 58449 of length 31: 54745 of length 32: 50602 of length 33: 47647 of length 34: 44708 of length 35: 41391 of length 36: 38898 of length 37: 36670 of length 38: 33928 of length 39: 31625 of length 40: 29424 of length 41: 27003 of length 42: 24774 of length 43: 21262 of length 44: 17067 of length 45: 12528 of length 46: 8265 of length 47: 5228 of length 48: 3358 of length 49: 1906 of length 50: 1224 In total 3436589 peptides. Generated 5723091 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 1.25 Da. 237499630 fragments to be searched in 1 slices (3.54 GB total) Operating on slice 1 of 1: Fragment index slice generated in 3.66 s

  1. DmWOL+Sperm1.mzBIN_calibrated 1.3 s [progress: 75329/75329 (100%) - 10732 spectra/s] 7.0s | remapping alternative proteins and postprocessing 19.4 s
  2. DmWOL+Sperm1_20210721183103.mzBIN_calibrated 1.9 s [progress: 76519/76519 (100%) - 11520 spectra/s] 6.6s | remapping alternative proteins and postprocessing 17.4 s
  3. DmWOL+Sperm1_20210721231700.mzBIN_calibrated 1.1 s [progress: 77687/77687 (100%) - 10835 spectra/s] 7.2s | remapping alternative proteins and postprocessing 16.1 s
  4. DmWOL-Sperm2.mzBIN_calibrated 1.7 s [progress: 118227/118227 (100%) - 9817 spectra/s] 12.0s | remapping alternative proteins and postprocessing 27.2 s
  5. DmWOL-Sperm2_20210722084851.mzBIN_calibrated 2.0 s [progress: 118298/118298 (100%) - 9983 spectra/s] 11.9s | remapping alternative proteins and postprocessing 23.5 s
  6. DmWOL-Sperm2_20210722133447.mzBIN_calibrated 1.6 s [progress: 121157/121157 (100%) - 10371 spectra/s] 11.7s | remapping alternative proteins and postprocessing 22.9 s MAIN SEARCH DONE IN 3.525 MIN

***TOTAL TIME 18.783 MIN**** Process 'MSFragger' finished, exit code: 0 MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2.pepXML /home/tlicknac/fragpipe_test/FP-out/wolM_1/DmWOL-Sperm2.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2.pin /home/tlicknac/fragpipe_test/FP-out/wolM_1/DmWOL-Sperm2.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722084851.pepXML /home/tlicknac/fragpipe_test/FP-out/wolM_2/DmWOL-Sperm2_20210722084851.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722084851.pin /home/tlicknac/fragpipe_test/FP-out/wolM_2/DmWOL-Sperm2_20210722084851.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722133447.pepXML /home/tlicknac/fragpipe_test/FP-out/wolM_3/DmWOL-Sperm2_20210722133447.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL-Sperm2_20210722133447.pin /home/tlicknac/fragpipe_test/FP-out/wolM_3/DmWOL-Sperm2_20210722133447.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1.pepXML /home/tlicknac/fragpipe_test/FP-out/wolP_1/DmWOL+Sperm1.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1.pin /home/tlicknac/fragpipe_test/FP-out/wolP_1/DmWOL+Sperm1.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721183103.pepXML /home/tlicknac/fragpipe_test/FP-out/wolP_2/DmWOL+Sperm1_20210721183103.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721183103.pin /home/tlicknac/fragpipe_test/FP-out/wolP_2/DmWOL+Sperm1_20210721183103.pin Process 'MSFragger move pin' finished, exit code: 0 MSFragger move pepxml java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721231700.pepXML /home/tlicknac/fragpipe_test/FP-out/wolP_3/DmWOL+Sperm1_20210721231700.pepXML Process 'MSFragger move pepxml' finished, exit code: 0 MSFragger move pin java -cp /home/tlicknac/software/fragpipe/lib/fragpipe-19.1.jar:/home/tlicknac/software/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err /home/tlicknac/fragpipe_test/DmWOL+Sperm1_20210721231700.pin /home/tlicknac/fragpipe_test/FP-out/wolP_3/DmWOL+Sperm1_20210721231700.pin Process 'MSFragger move pin' finished, exit code: 0 MSBooster [Work dir: /home/tlicknac/fragpipe_test/FP-out] java -Xmx114G -cp /home/tlicknac/software/fragpipe/tools/msbooster-1.1.11.jar:/home/tlicknac/software/fragpipe/tools/batmass-io-1.28.9.jar Features.MainClass --paramsList /home/tlicknac/fragpipe_test/FP-out/msbooster_params.txt Process 'MSBooster' finished, exit code: 132 Process returned non-zero exit code, stopping


Cancelling 53 remaining tasks
yangkl96 commented 1 year ago

Hello,

Error code 132 might indicate a corrupt file. Could you try redownloading FragPipe and running it again?

If not that, it might be a system issue. You could try running on your own computer off the cluster? Or copying this command and running it on command line from /home/tlicknac/fragpipe_test/FP-out/: java -Xmx114G -cp /home/tlicknac/software/fragpipe/tools/msbooster-1.1.11.jar:/home/tlicknac/software/fragpipe/tools/batmass-io-1.28.9.jar Features.MainClass --paramsList /home/tlicknac/fragpipe_test/FP-out/msbooster_params.txt

Let me know how it goes, Kevin