Zero ID crashes Percolator: exit code: -1073741819

Raghothama1 commented 9 months ago

Describe the issue or question: Batmass-IO version 1.28.12 WARNING: An illegal reflective access operation has occurred WARNING: Illegal reflective access by org.nustaq.serialization.FSTClazzInfo (file:/C:/Software/FragPipe/FragPipe-jre-20.0/fragpipe/tools/DIA_Umpire_SE-2.3.2.jar) to field java.lang.String.value WARNING: Please consider reporting this to the maintainers of org.nustaq.serialization.FSTClazzInfo WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations WARNING: All illegal access operations will be denied in a future release 2023-09-30 22:39:43 log_2023-10-01_08-20-04.txt
Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

fcyu commented 9 months ago

Your error message is Process 'Percolator' finished, exit code: -1073741819, which is the same as https://github.com/Nesvilab/FragPipe/issues/1227, https://github.com/Nesvilab/FragPipe/issues/1211, and https://github.com/Nesvilab/FragPipe/issues/1160.

There is no ID in your data. Since you were using DIA-Umpire, could you try another workflow, DIA_SpecLib_Quant, to use MSFragger-DIA rather than DIA-Umpire?

Best,

Fengchao

Raghothama1 commented 9 months ago

Hi Fengchao, I got the same error message when I selected MSFragger-DIA. Do you mind checking the log file? My dataset has only DIA raw files no DDA files for library construction. Thanks a lot Raghothama

From: Fengchao @.> Sent: Sunday, October 1, 2023 1:49 PM To: Nesvilab/FragPipe @.> Cc: Raghothama1 @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Error during DIA-MS runs (Issue #1269)

Closed #1269https://github.com/Nesvilab/FragPipe/issues/1269 as completed.

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1269#event-10519681300, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BC6ZSXO5ZHRCHODAM2GMDIDX5FYILANCNFSM6AAAAAA5OKMYQA. You are receiving this because you authored the thread.Message ID: @.***>

System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: N/A

Version info: FragPipe version 20.0 MSFragger version 3.8 IonQuant version 1.9.8 Philosopher version 5.0.0

LCMS files: Experiment/Group:

C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1.raw DIA
C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_330-430_1.raw DIA
C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_428-528_1.raw DIA
C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_528_628_1.raw DIA
C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_628-728_1.raw DIA
C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_728-828_1.raw DIA
C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_828-928_1.raw DIA
C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_928-1028_1.raw DIA

45 commands to execute: CheckCentroid C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx38G -cp "C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar;C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1.raw 7 WorkspaceCleanInit [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\14108\AppData\Local\Temp\cbb26772-ed96-4b81-87d3-f69411417a3d MSFragger [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx38G C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\fragger_dia.params C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_330-430_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_428-528_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_528_628_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_628-728_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_728-828_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_828-928_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_928-1028_1.raw MSBooster [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx38G -cp "C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\msbooster-1.1.11.jar;C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\msbooster_params.txt Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_628-728_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_628-728_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_628-728_1_edited.pin Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_428-528_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_428-528_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_428-528_1_edited.pin Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_728-828_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_728-828_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_728-828_1_edited.pin Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_828-928_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_828-928_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_828-928_1_edited.pin Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_330-430_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_330-430_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_330-430_1_edited.pin Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_528_628_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_528_628_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_528_628_1_edited.pin Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_1028_1128_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_1028_1128_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_1028_1128_1_edited.pin Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_928-1028_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_928-1028_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_928-1028_1_edited.pin Percolator: Convert to pepxml [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230930_deplPlasma-DIA_120min_628-728_1.pin 20230930_deplPlasma-DIA_120min_628-728_1 20230930_deplPlasma-DIA_120min_628-728_1_percolator_target_psms.tsv 20230930_deplPlasma-DIA_120min_628-728_1_percolator_decoy_psms.tsv interact-20230930_deplPlasma-DIA_120min_628-728_1 DIA 0.7 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_628-728_1_uncalibrated.mzML Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_628-728_1_percolator_target_psms.tsv Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_628-728_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230930_deplPlasma-DIA_120min_428-528_1.pin 20230930_deplPlasma-DIA_120min_428-528_1 20230930_deplPlasma-DIA_120min_428-528_1_percolator_target_psms.tsv 20230930_deplPlasma-DIA_120min_428-528_1_percolator_decoy_psms.tsv interact-20230930_deplPlasma-DIA_120min_428-528_1 DIA 0.7 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_428-528_1_uncalibrated.mzML Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_428-528_1_percolator_target_psms.tsv Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_428-528_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230930_deplPlasma-DIA_120min_728-828_1.pin 20230930_deplPlasma-DIA_120min_728-828_1 20230930_deplPlasma-DIA_120min_728-828_1_percolator_target_psms.tsv 20230930_deplPlasma-DIA_120min_728-828_1_percolator_decoy_psms.tsv interact-20230930_deplPlasma-DIA_120min_728-828_1 DIA 0.7 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_728-828_1_uncalibrated.mzML Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_728-828_1_percolator_target_psms.tsv Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_728-828_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230930_deplPlasma-DIA_120min_828-928_1.pin 20230930_deplPlasma-DIA_120min_828-928_1 20230930_deplPlasma-DIA_120min_828-928_1_percolator_target_psms.tsv 20230930_deplPlasma-DIA_120min_828-928_1_percolator_decoy_psms.tsv interact-20230930_deplPlasma-DIA_120min_828-928_1 DIA 0.7 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_828-928_1_uncalibrated.mzML Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_828-928_1_percolator_target_psms.tsv Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_828-928_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230930_deplPlasma-DIA_120min_330-430_1.pin 20230930_deplPlasma-DIA_120min_330-430_1 20230930_deplPlasma-DIA_120min_330-430_1_percolator_target_psms.tsv 20230930_deplPlasma-DIA_120min_330-430_1_percolator_decoy_psms.tsv interact-20230930_deplPlasma-DIA_120min_330-430_1 DIA 0.7 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_330-430_1_uncalibrated.mzML Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_330-430_1_percolator_target_psms.tsv Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_330-430_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230930_deplPlasma-DIA_120min_528_628_1.pin 20230930_deplPlasma-DIA_120min_528_628_1 20230930_deplPlasma-DIA_120min_528_628_1_percolator_target_psms.tsv 20230930_deplPlasma-DIA_120min_528_628_1_percolator_decoy_psms.tsv interact-20230930_deplPlasma-DIA_120min_528_628_1 DIA 0.7 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_528_628_1_uncalibrated.mzML Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_528_628_1_percolator_target_psms.tsv Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_528_628_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230930_deplPlasma-DIA_120min_1028_1128_1.pin 20230930_deplPlasma-DIA_120min_1028_1128_1 20230930_deplPlasma-DIA_120min_1028_1128_1_percolator_target_psms.tsv 20230930_deplPlasma-DIA_120min_1028_1128_1_percolator_decoy_psms.tsv interact-20230930_deplPlasma-DIA_120min_1028_1128_1 DIA 0.7 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1_uncalibrated.mzML Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1_percolator_target_psms.tsv Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML 20230930_deplPlasma-DIA_120min_928-1028_1.pin 20230930_deplPlasma-DIA_120min_928-1028_1 20230930_deplPlasma-DIA_120min_928-1028_1_percolator_target_psms.tsv 20230930_deplPlasma-DIA_120min_928-1028_1_percolator_decoy_psms.tsv interact-20230930_deplPlasma-DIA_120min_928-1028_1 DIA 0.7 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_928-1028_1_uncalibrated.mzML Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_928-1028_1_percolator_target_psms.tsv Percolator: Delete temp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -cp C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_928-1028_1_percolator_decoy_psms.tsv ProteinProphet [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe database --annotate C:\temp_data\Plasma_Serum_DIA\Fragpipe\2023-09-24-decoys-contam-Human_20386May2022.fasta.fas --prefix rev PhilosopherFilter [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --picked --prot 0.01 --tag rev --pepxml C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da --protxml C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\combined.prot.xml --razor PhilosopherReport [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report SpecLibGen [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Users\14108\AppData\Local\Programs\Python\Python311\python -u C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\speclib\gen_con_spec_lib.py C:\temp_data\Plasma_Serum_DIA\Fragpipe\2023-09-24-decoys-contam-Human_20386_May2022.fasta.fas C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da unused C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da True unused use_easypqp noiRT;noIM 7 "--max_delta_unimod 0.02 --max_delta_ppm 15.0 --fragment_types [\'b\',\'y\',] " "--rt_lowess_fraction 0.0" keep_intermediate_files C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\filelist_speclibgen.txt DIA-NN [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib library.tsv --threads 7 --verbose 1 --out diann-output\diann-output.tsv --qvalue 0.01 --matrix-qvalue 0.01 --matrices --no-prot-inf --smart-profiling --no-quant-files --peak-center --no-ifs-removal --predictor --dl-no-rt --dl-no-im --strip-unknown-mods --cfg C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\filelist_diann.txt DIA-NN [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\diann\1.8.2_beta_8\win\dia-nn-plotter.exe diann-output\diann-output.stats.tsv diann-output\diann-output.tsv diann-output\diann-output.pdf WorkspaceClean [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [CheckCentroid], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [MSFragger], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [MSBooster], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [Percolator], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [ProteinProphet], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [PhilosopherDbAnnotate], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [PhilosopherFilter], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [PhilosopherReport], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [SpecLibGen], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [DIA-NN], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]
    Cmd: [WorkspaceClean], Work dir: [C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da]

>rev_sp|A0A024RBG1|NUD4B_HUMAN Diphosphoinositol polyphosphate phosphohydrolase NUDT4B OS=Homo sapiens OX=9606 GN=NUDT4B PE=3 SV=1
>rev_sp|O43929|ORC4_HUMAN Origin recognition complex subunit 4 OS=Homo sapiens OX=9606 GN=ORC4 PE=1 SV=2
>rev_sp|P0DPI4|TDB01_HUMAN T cell receptor beta diversity 1 OS=Homo sapiens OX=9606 GN=TRBD1 PE=4 SV=1
>rev_sp|P50458|LHX2_HUMAN LIM/homeobox protein Lhx2 OS=Homo sapiens OX=9606 GN=LHX2 PE=1 SV=2
>rev_sp|Q14493|SLBP_HUMAN Histone RNA hairpin-binding protein OS=Homo sapiens OX=9606 GN=SLBP PE=1 SV=1
>rev_sp|Q6E213|AWAT2_HUMAN Acyl-CoA wax alcohol acyltransferase 2 OS=Homo sapiens OX=9606 GN=AWAT2 PE=1 SV=1
>rev_sp|Q8IXA5|SACA3_HUMAN Sperm acrosome membrane-associated protein 3 OS=Homo sapiens OX=9606 GN=SPACA3 PE=1 SV=1
>rev_sp|Q8WWL2|SPIR2_HUMAN Protein spire homolog 2 OS=Homo sapiens OX=9606 GN=SPIRE2 PE=1 SV=3
>rev_sp|Q9BS86|ZPBP1_HUMAN Zona pellucida-binding protein 1 OS=Homo sapiens OX=9606 GN=ZPBP PE=2 SV=1
>rev_sp|Q9NVJ2|ARL8B_HUMAN ADP-ribosylation factor-like protein 8B OS=Homo sapiens OX=9606 GN=ARL8B PE=1 SV=1
>rev_sp|W5XKT8|SACA6_HUMAN Sperm acrosome membrane-associated protein 6 OS=Homo sapiens OX=9606 GN=SPACA6 PE=1 SV=2
>sp|O43920|NDUS5_HUMAN NADH dehydrogenase [ubiquinone] iron-sulfur protein 5 OS=Homo sapiens OX=9606 GN=NDUFS5 PE=1 SV=3
>sp|P0DPH8|TBA3D_HUMAN Tubulin alpha-3D chain OS=Homo sapiens OX=9606 GN=TUBA3D PE=1 SV=1
>sp|P50443|S26A2_HUMAN Sulfate transporter OS=Homo sapiens OX=9606 GN=SLC26A2 PE=1 SV=2
>sp|Q14449|GRB14_HUMAN Growth factor receptor-bound protein 14 OS=Homo sapiens OX=9606 GN=GRB14 PE=1 SV=2
>sp|Q6DRA6|H2B2D_HUMAN Putative histone H2B type 2-D OS=Homo sapiens OX=9606 GN=H2BC19P PE=5 SV=3
>sp|Q8IX30|SCUB3_HUMAN Signal peptide, CUB and EGF-like domain-containing protein 3 OS=Homo sapiens OX=9606 GN=SCUBE3 PE=1 SV=1
>sp|Q8WWH5|TRUB1_HUMAN Pseudouridylate synthase TRUB1 OS=Homo sapiens OX=9606 GN=TRUB1 PE=1 SV=1
>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens OX=9606 GN=ERP44 PE=1 SV=1
>sp|Q9NVH2|INT7_HUMAN Integrator complex subunit 7 OS=Homo sapiens OX=9606 GN=INTS7 PE=1 SV=1
>sp|Q9YNA8|GAK19_HUMAN Endogenous retrovirus group K member 19 Gag polyprotein OS=Homo sapiens OX=9606 GN=ERVK-19 PE=1 SV=3

# FragPipe v20.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=C\:\\temp_data\\Plasma_Serum_DIA\\Fragpipe\\2023-09-24-decoys-contam-Human_20386_May2022.fasta.fas

crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.heavy=
diann.library=
diann.light=
diann.medium=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=true
diann.run-dia-plex=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=20
diaumpire.SE.MS2PPM=30
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=C\:\\Software\\FragPipe\\FragPipe-jre-20.0\\fragpipe\\tools\\IonQuant-1.9.8.jar
fragpipe-config.bin-msfragger=C\:\\Software\\FragPipe\\FragPipe-jre-20.0\\fragpipe\\tools\\MSFragger-3.8\\MSFragger-3.8.jar
fragpipe-config.bin-philosopher=C\:\\Software\\FragPipe\\FragPipe-jre-20.0\\fragpipe\\tools\\philosopher_v5.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\Users\\14108\\AppData\\Local\\Programs\\Python\\Python311\\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=1
ionquant.mbr=0
ionquant.mbrimtol=0.05
ionquant.mbrmincorr=0
ionquant.mbrrttol=1
ionquant.mbrtoprun=10
ionquant.medium=
ionquant.minfreq=0
ionquant.minions=1
ionquant.minisotopes=1
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=1
msfragger.allowed_missed_cleavage_2=1
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.group_variable=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=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=5
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.00
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.output_report_topN_dia1=5
msfragger.output_report_topN_dia2=3
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.require_precursor=true
msfragger.restrict_deltamass_to=all
msfragger.reuse_dia_fragment_peaks=false
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; 0.984016,N,true,2; 0.984016,Q,true,2; 0.0,site_08,false,1; 0.0,site_09,false,1; 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=300
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.filterOxonium=true
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.oxonium_filtering_file=
opair.oxonium_minimum_intensity=0.05
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=0.7
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--picked --prot 0.01
phi-report.pep-level-summary=false
phi-report.philosoher-msstats=false
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 --minprob 0.5
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=
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=25
ptmshepherd.diagmine_fragMinFoldChange=3.0
ptmshepherd.diagmine_fragMinPropensity=12.5
ptmshepherd.diagmine_fragMinSpecDiff=25
ptmshepherd.diagmine_minIonsPerSpec=2
ptmshepherd.diagmine_minPeps=25
ptmshepherd.diagmine_mode=false
ptmshepherd.diagmine_pepMinFoldChange=3.0
ptmshepherd.diagmine_pepMinSpecDiff=25
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=true
ptmshepherd.iontype_x=false
ptmshepherd.iontype_y=true
ptmshepherd.iontype_z=true
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=false
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=true
speclibgen.run-speclibgen=true
tab-run.delete_calibrated_mzml=false
tab-run.delete_temp_files=false
tab-run.sub_mzml_prob_threshold=0.5
tab-run.write_sub_mzml=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=C\:\\temp_data\\RC-DIA-MS\\DIA_MS_120min_2-2da
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=7

CheckCentroid C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx38G -cp "C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\lib\fragpipe-20.0.jar;C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1.raw 7 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[13:22:49] Executing Workspace v5.0.0
INFO[13:22:49] Removing workspace
WARN[13:22:49] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[13:22:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\14108\AppData\Local\Temp\cbb26772-ed96-4b81-87d3-f69411417a3d INFO[13:22:49] Executing Workspace v5.0.0
INFO[13:22:49] Creating workspace
INFO[13:22:49] Done
Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx38G C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\fragger_dia.params C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_330-430_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_428-528_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_528_628_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_628-728_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_728-828_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_828-928_1.raw C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_928-1028_1.raw MSFragger version MSFragger-3.8 Batmass-IO version 1.28.12 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: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK JVM started with 38 GB memory Checking database... data_type > 0. Will use the isolation window from the spectral file as precursor tolerance. Checking spectral files... C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1.raw: Scans = 35014 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_330-430_1.raw: Scans = 48056 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_628-728_1.raw: Scans = 49121 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_728-828_1.raw: Scans = 48773 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_428-528_1.raw: Scans = 49780 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_528_628_1.raw: Scans = 48148 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_828-928_1.raw: Scans = 48870 C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_928-1028_1.raw: Scans = 35532 ***FIRST SEARCH**** Parameters: num_threads = 7 database_name = C:\temp_data\Plasma_Serum_DIA\Fragpipe\2023-09-24-decoys-contam-Human_20386_May2022.fasta.fas decoyprefix = rev precursor_mass_lower = -10.0 precursor_mass_upper = 10.0 precursor_mass_units = 1 data_type = 1 precursor_true_tolerance = 10.0 precursor_true_units = 1 fragment_mass_tolerance = 20.0 fragment_mass_units = 1 calibrate_mass = 1 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 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 = 1 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 1 output_max_expect = 1.7976931348623157E308 report_alternative_proteins = 0 override_charge = 1 precursor_charge_low = 2 precursor_charge_high = 3 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 deneutralloss = 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 = 200 minIonsScoring = 2 min_matched_fragments = 5 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = isolation window 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 = 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 Selected fragment index width 0.10 Da. 96041580 fragments to be searched in 1 slices (1.43 GB total) Operating on slice 1 of 1: Fragment index slice generated in 1.24 s

20230930_deplPlasma-DIA_120min_1028_1128_1.raw 15.8 s | deisotoping 0.5 s [progress: 33731/33731 (100%) - 12899 spectra/s] 2.6s
20230930_deplPlasma-DIA_120min_330-430_1.raw 14.4 s | deisotoping 0.1 s [progress: 48018/48018 (100%) - 8984 spectra/s] 5.3s
20230930_deplPlasma-DIA_120min_428-528_1.raw 20.5 s | deisotoping 0.3 s [progress: 49231/49231 (100%) - 5223 spectra/s] 9.4s
20230930_deplPlasma-DIA_120min_528_628_1.raw 20.7 s | deisotoping 0.3 s [progress: 47314/47314 (100%) - 4916 spectra/s] 9.6s
20230930_deplPlasma-DIA_120min_628-728_1.raw 21.3 s | deisotoping 0.3 s [progress: 47744/47744 (100%) - 5622 spectra/s] 8.5s
20230930_deplPlasma-DIA_120min_728-828_1.raw 20.2 s | deisotoping 0.4 s [progress: 47549/47549 (100%) - 6891 spectra/s] 6.9s
20230930_deplPlasma-DIA_120min_828-928_1.raw 18.0 s | deisotoping 0.2 s [progress: 47042/47042 (100%) - 8813 spectra/s] 5.3s
20230930_deplPlasma-DIA_120min_928-1028_1.raw 12.5 s | deisotoping 0.1 s [progress: 34285/34285 (100%) - 13086 spectra/s] 2.6s ***FIRST SEARCH DONE IN 3.675 MIN**

*******MASS CALIBRATION -----	---------------	---------------
Run	Median MAD	Median MAD
001	1.60 1.64	0.07 1.69
002	-0.56 1.10	-0.01 1.03
003	-0.22 0.85	-0.03 0.73
004	1.74 0.95	-0.03 0.85
005	1.86 1.12	-0.05 1.04
006	1.99 1.27	-0.01 1.22
007	2.03 1.32	-0.02 1.32
008	1.78 1.53	0.08 1.57
-----	---------------	---------------

New fragment_mass_tolerance = 7 PPM **MASS CALIBRATION DONE IN 1.109 MIN***

****MAIN SEARCH**** Checking database... data_type > 0. Will use the isolation window from the spectral file as precursor tolerance. Parameters: num_threads = 7 database_name = C:\temp_data\Plasma_Serum_DIA\Fragpipe\2023-09-24-decoys-contam-Human_20386_May2022.fasta.fas decoyprefix = rev precursor_mass_lower = -10.0 precursor_mass_upper = 10.0 precursor_mass_units = 1 data_type = 1 precursor_true_tolerance = 10.0 precursor_true_units = 1 fragment_mass_tolerance = 7.0 fragment_mass_units = 1 calibrate_mass = 1 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0 mass_offsets = 0 labile_search_mode = OFF restrict_deltamass_to = all precursor_mass_mode = SELECTED localize_delta_mass = 0 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 = 1 num_enzyme_termini = 2 clip_nTerm_M = 1 allow_multiple_variable_mods_on_residue = 0 max_variable_mods_per_peptide = 3 max_variable_mods_combinations = 5000 output_format = pepxml_pin output_report_topN = 5 output_max_expect = 1.7976931348623157E308 report_alternative_proteins = 1 override_charge = 1 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 deneutralloss = 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 = 300 minIonsScoring = 2 min_matched_fragments = 5 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 1 remove_precursor_range = isolation window 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 = 1 variable_mod_01 = 15.9949 M 3 variable_mod_02 = 42.0106 [^ 1 variable_mod_06 = 0.984016 N 2 variable_mod_07 = 0.984016 Q 2 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: 238603 of length 8: 221801 of length 9: 214395 of length 10: 193568 of length 11: 177430 of length 12: 163505 of length 13: 153504 of length 14: 138483 of length 15: 127227 of length 16: 115909 of length 17: 105747 of length 18: 97526 of length 19: 91906 of length 20: 82421 of length 21: 76870 of length 22: 69809 of length 23: 64893 of length 24: 60214 of length 25: 55825 of length 26: 50996 of length 27: 48275 of length 28: 43886 of length 29: 40842 of length 30: 38106 of length 31: 34513 of length 32: 32165 of length 33: 29531 of length 34: 27029 of length 35: 24553 of length 36: 23179 of length 37: 20470 of length 38: 19252 of length 39: 16974 of length 40: 16221 of length 41: 15073 of length 42: 13476 of length 43: 11397 of length 44: 9383 of length 45: 7411 of length 46: 4940 of length 47: 3208 of length 48: 1946 of length 49: 1116 of length 50: 689 In total 2984267 peptides. Generated 20682148 modified peptides. Number of peptides with more than 5000 modification patterns: 0 Selected fragment index width 0.03 Da. 995936720 fragments to be searched in 1 slices (14.84 GB total) Operating on slice 1 of 1: Fragment index slice generated in 13.02 s

20230930_deplPlasma-DIA_120min_1028_1128_1.mzBIN_calibrated 0.4 s [progress: 33722/33722 (100%) - 2262 spectra/s] 14.9s Building spectral index for the mzBIN_calibrated file 2.8 s Rescoring with peak tracing 0.3 s Picking top PSMs for each precursor 0.0 s Rescoring 0.0 s Writing results 0.1 s
20230930_deplPlasma-DIA_120min_330-430_1.mzBIN_calibrated 0.6 s [progress: 47928/47928 (100%) - 2172 spectra/s] 22.1s Building spectral index for the mzBIN_calibrated file 2.9 s Rescoring with peak tracing 6.5 s Picking top PSMs for each precursor 0.1 s Rescoring 0.1 s Writing results 0.6 s
20230930_deplPlasma-DIA_120min_428-528_1.mzBIN_calibrated 0.7 s [progress: 48981/48981 (100%) - 1081 spectra/s] 45.3s Building spectral index for the mzBIN_calibrated file 3.5 s Rescoring with peak tracing 5.1 s Picking top PSMs for each precursor 0.3 s Rescoring 0.2 s Writing results 1.0 s
20230930_deplPlasma-DIA_120min_528_628_1.mzBIN_calibrated 0.7 s [progress: 47204/47204 (100%) - 884 spectra/s] 53.4s Building spectral index for the mzBIN_calibrated file 4.0 s Rescoring with peak tracing 7.2 s Picking top PSMs for each precursor 0.2 s Rescoring 0.2 s Writing results 1.3 s
20230930_deplPlasma-DIA_120min_628-728_1.mzBIN_calibrated 0.7 s [progress: 47692/47692 (100%) - 938 spectra/s] 50.9s Building spectral index for the mzBIN_calibrated file 3.8 s Rescoring with peak tracing 7.5 s Picking top PSMs for each precursor 0.2 s Rescoring 0.3 s Writing results 1.0 s
20230930_deplPlasma-DIA_120min_728-828_1.mzBIN_calibrated 0.7 s [progress: 47536/47536 (100%) - 1034 spectra/s] 46.0s Building spectral index for the mzBIN_calibrated file 3.7 s Rescoring with peak tracing 6.6 s Picking top PSMs for each precursor 0.1 s Rescoring 0.1 s Writing results 0.9 s
20230930_deplPlasma-DIA_120min_828-928_1.mzBIN_calibrated 0.6 s [progress: 47014/47014 (100%) - 1142 spectra/s] 41.2s Building spectral index for the mzBIN_calibrated file 3.2 s Rescoring with peak tracing 5.8 s Picking top PSMs for each precursor 0.1 s Rescoring 0.1 s Writing results 0.8 s
20230930_deplPlasma-DIA_120min_928-1028_1.mzBIN_calibrated 0.4 s [progress: 34271/34271 (100%) - 1623 spectra/s] 21.1s Building spectral index for the mzBIN_calibrated file 2.4 s Rescoring with peak tracing 0.3 s Picking top PSMs for each precursor 0.0 s Rescoring 0.0 s Writing results 0.0 s MAIN SEARCH DONE IN 7.380 MIN

***TOTAL TIME 12.165 MIN**** Process 'MSFragger' finished, exit code: 0 MSBooster [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\jre\bin\java.exe -Xmx38G -cp "C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\msbooster-1.1.11.jar;C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\msbooster_params.txt MSBooster v1.1.11 Using 7 threads Generating input file for DIA-NN 86846 unique peptides from 100233 PSMs Writing DIA-NN input file Diann input file generation took 969 milliseconds Input file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\spectraRT.tsv 91888 unique peptides from 100233 PSMs createFull input file generation took 437 milliseconds Input file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\spectraRT_full.tsv Generating DIA-NN predictions C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\diann\1.8.2_beta_8\win\DiaNN.exe --lib C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\spectraRT.tsv --predict --threads 7 --strip-unknown-mods --mod TMT,229.1629 --predict-n-frag 100 DIA-NN 1.8.2 beta 8 (Data-Independent Acquisition by Neural Networks) Compiled on Sep 15 2022 18:28:57 Current date and time: Tue Oct 3 13:35:03 2023 CPU: GenuineIntel Intel(R) Core(TM) i7-9700K CPU @ 3.60GHz SIMD instructions: AVX AVX2 FMA SSE4.1 SSE4.2 Logical CPU cores: 8 Predicted spectra will be saved in a binary format Thread number set to 7 DIA-NN will use deep learning to predict spectra/RTs/IMs even for peptides carrying modifications which are not recognised by the deep learning predictor. In this scenario, if also generating a spectral library from the DIA data or using the MBR mode, it might or might not be better (depends on the data) to also use the --out-measured-rt option - it's recommended to test it with and without this option Modification TMT with mass delta 229.163 added to the list of recognised modifications for spectral library-based search Deep learning predictor will predict 100 fragments Cannot find a UniMod modification match for TMT: 73.0618 minimal mass discrepancy; using the original modificaiton name

0 files will be processed [0:00] Loading spectral library C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\spectraRT.tsv [0:00] Finding proteotypic peptides (assuming that the list of UniProt ids provided for each peptide is complete) [0:00] Spectral library loaded: 0 protein isoforms, 0 protein groups and 86846 precursors in 83100 elution groups. [0:00] Encoding peptides for spectra and RTs prediction [0:00] Predicting spectra and IMs [0:27] Predicting RTs [0:35] Decoding predicted spectra and IMs [0:37] Decoding RTs [0:37] Saving the list of predictions to C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\spectraRT.predicted.bin Finished Done generating DIA-NN predictions Model running took 39261 milliseconds Generating edited pin with following features: [unweightedSpectralEntropy, deltaRTLOESS] Loading predicted spectra Processing 20230930_deplPlasma-DIA_120min_1028_1128_1_uncalibrated.mzML Not enough high quality PSMs for RT regression. Removing escore cutoff Warning: not enough target PSMs are available for regression, setting RT scores equal to 0 Edited pin file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_1028_1128_1_edited.pin Processing 20230930_deplPlasma-DIA_120min_330-430_1_uncalibrated.mzML RT regression using 4850 PSMs Edited pin file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_330-430_1_edited.pin Processing 20230930_deplPlasma-DIA_120min_428-528_1_uncalibrated.mzML RT regression using 5000 PSMs Edited pin file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_428-528_1_edited.pin Processing 20230930_deplPlasma-DIA_120min_528_628_1_uncalibrated.mzML RT regression using 5000 PSMs Edited pin file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_528_628_1_edited.pin Processing 20230930_deplPlasma-DIA_120min_628-728_1_uncalibrated.mzML RT regression using 5000 PSMs Edited pin file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_628-728_1_edited.pin Processing 20230930_deplPlasma-DIA_120min_728-828_1_uncalibrated.mzML RT regression using 5000 PSMs Edited pin file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_728-828_1_edited.pin Processing 20230930_deplPlasma-DIA_120min_828-928_1_uncalibrated.mzML RT regression using 5000 PSMs Edited pin file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_828-928_1_edited.pin Processing 20230930_deplPlasma-DIA_120min_928-1028_1_uncalibrated.mzML RT regression using 229 PSMs Edited pin file at C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da\20230930_deplPlasma-DIA_120min_928-1028_1_edited.pin Done in 21299 ms Process 'MSBooster' finished, exit code: 0 Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_628-728_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_628-728_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_628-728_1_edited.pin Protein decoy-preix used is rev_sp| All files have been read Percolator version 3.06.0, Build Date May 11 2022 12:43:39 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll @.) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_628-728_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_628-728_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_628-728_1_edited.pin Started Tue Oct 3 13:36:03 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230930_deplPlasma-DIA_120min_628-728_1_edited.pin Features: rank log10_intensity abs_ppm abs_rt_diff complementary_ions ion_series weighted_average_abs_fragment_ppm weighted_average_fragment_rt_deviation precursor_rt_deviation isotopes log10_kl log10_kl_negative_1 log10_kl_negative_2 hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 0.984016N 0.984016Q 15.9949M unweighted_spectral_entropy delta_RT_loess Found 21212 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 12368 positives and 8844 negatives, size ratio=1.39846 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 33 as initial direction. Could separate 1635 training set positives with q<0.01 in that direction. Split 2: Selected feature 33 as initial direction. Could separate 1673 training set positives with q<0.01 in that direction. Split 3: Selected feature 33 as initial direction. Could separate 1781 training set positives with q<0.01 in that direction. Found 2471 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.3670 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 3034 PSMs with q<0.01 Iteration 2: Estimated 3078 PSMs with q<0.01 Iteration 3: Estimated 3095 PSMs with q<0.01 Iteration 4: Estimated 3100 PSMs with q<0.01 Iteration 5: Estimated 3092 PSMs with q<0.01 Iteration 6: Estimated 3092 PSMs with q<0.01 Iteration 7: Estimated 3093 PSMs with q<0.01 Iteration 8: Estimated 3094 PSMs with q<0.01 Iteration 9: Estimated 3090 PSMs with q<0.01 Iteration 10: Estimated 3092 PSMs with q<0.01 Learned normalized SVM weights for the 3 cross-validation splits: Split1 Split2 Split3 FeatureName -0.0126 -0.1485 -0.1518 rank -0.0358 -0.0101 0.2053 log10_intensity -0.0552 -0.2007 -0.0119 abs_ppm 0.0355 -0.0319 -0.0031 abs_rt_diff -0.2033 -0.2192 -0.2962 complementary_ions 0.1629 0.4567 0.3161 ion_series 0.0213 -0.0145 -0.0371 weighted_average_abs_fragment_ppm 0.0361 -0.0251 -0.0647 weighted_average_fragment_rt_deviation -0.0678 -0.0714 -0.0742 precursor_rt_deviation 0.2112 0.1602 0.2793 isotopes 0.0085 -0.1533 0.1925 log10_kl -0.0675 -0.0101 -0.1596 log10_kl_negative_1 0.0251 0.0781 0.0521 log10_kl_negative_2 0.5339 0.9366 1.4144 hyperscore 0.0514 -0.2767 -0.9758 matched_ion_num -0.2139 -0.0692 -0.7255 peptide_length 0.0000 0.0000 0.0000 ntt -0.0459 -0.2439 -0.1197 nmc -0.4122 -0.7145 -0.8167 charge_1 -0.0642 -0.1582 -0.4101 charge_2 0.0782 0.2737 0.2424 charge_3 0.1264 0.1215 0.4404 charge_4 0.0000 0.0000 0.0000 charge_5 0.0000 0.0000 0.0000 charge_6 0.0000 0.0000 0.0000 charge_7_or_more 0.0000 0.0000 0.0000 group_1 0.0000 0.0000 0.0000 group_2 0.0000 0.0000 0.0000 group_3 0.0000 0.0000 0.0000 group_other -0.0809 -0.1753 -0.0282 0.984016N -0.1684 -0.4965 -0.2058 0.984016Q -0.1291 -0.2161 -0.2936 15.9949M 1.9911 2.9236 3.5536 unweighted_spectral_entropy 0.0000 0.0000 0.0000 delta_RT_loess -2.9370 -4.1491 -5.1135 m0 Found 3000 test set PSMs with q<0.01. Selected best-scoring PSM per scan+expMass (target-decoy competition): 12368 target PSMs and 8844 decoy PSMs. Calculating q values. Final list yields 3001 target PSMs with q<0.01. Calculating posterior error probabilities (PEPs). Processing took 2.6020 cpu seconds or 3 seconds wall clock time. Process 'Percolator' finished, exit code: 0 Percolator [Work dir: C:\temp_data\RC-DIA-MS\DIA_MS_120min_2-2da] C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_428-528_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_428-528_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_428-528_1_edited.pin Protein decoy-preix used is rev_sp| All files have been read Percolator version 3.06.0, Build Date May 11 2022 12:43:39 Copyright (c) 2006-9 University of Washington. All rights reserved. Written by Lukas Käll @.) in the Department of Genome Sciences at the University of Washington. Issued command: C:\Software\FragPipe\FragPipe-jre-20.0\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms 20230930_deplPlasma-DIA_120min_428-528_1_percolator_target_psms.tsv --decoy-results-psms 20230930_deplPlasma-DIA_120min_428-528_1_percolator_decoypsms.tsv --protein-decoy-pattern rev 20230930_deplPlasma-DIA_120min_428-528_1_edited.pin Started Tue Oct 3 13:36:06 2023 Hyperparameters: selectionFdr=0.01, Cpos=0, Cneg=0, maxNiter=10 Reading tab-delimited input from datafile 20230930_deplPlasma-DIA_120min_428-528_1_edited.pin Features: rank log10_intensity abs_ppm abs_rt_diff complementary_ions ion_series weighted_average_abs_fragment_ppm weighted_average_fragment_rt_deviation precursor_rt_deviation isotopes log10_kl log10_kl_negative_1 log10_kl_negative_2 hyperscore matched_ion_num peptide_length ntt nmc charge_1 charge_2 charge_3 charge_4 charge_5 charge_6 charge_7_or_more group_1 group_2 group_3 group_other 0.984016N 0.984016Q 15.9949M unweighted_spectral_entropy delta_RT_loess Found 16178 PSMs Concatenated search input detected and --post-processing-tdc flag set. Applying target-decoy competition on Percolator scores. Train/test set contains 9443 positives and 6735 negatives, size ratio=1.40208 and pi0=1 Selecting Cpos by cross-validation. Selecting Cneg by cross-validation. Split 1: Selected feature 14 as initial direction. Could separate 519 training set positives with q<0.01 in that direction. Split 2: Selected feature 14 as initial direction. Could separate 669 training set positives with q<0.01 in that direction. Split 3: Selected feature 14 as initial direction. Could separate 661 training set positives with q<0.01 in that direction. Found 711 test set positives with q<0.01 in initial direction Reading in data and feature calculation took 0.2690 cpu seconds or 0 seconds wall clock time. ---Training with Cpos selected by cross validation, Cneg selected by cross validation, initial_fdr=0.01, fdr=0.01 Iteration 1: Estimated 1638 PSMs with q<0.01 Iteration 2: Estimated 2019 PSMs with q<0.01

fcyu commented 9 months ago

Your log was truncated by GitHub. Could you zip and upload it here?

Thanks,

Fengchao

Raghothama1 commented 9 months ago

Attached, thank you for your time Raghothama

From: Fengchao @.> Sent: Tuesday, October 3, 2023 6:30 PM To: Nesvilab/FragPipe @.> Cc: Raghothama1 @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Zero ID crashes Percolator: exit code: -1073741819 (Issue #1269)

Your log was truncated by GitHub. Could you zip and upload it here?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/1269#issuecomment-1745508282, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BC6ZSXLILBRQRI4J5URKL5DX5RKTJAVCNFSM6AAAAAA5OKMYQCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBVGUYDQMRYGI. You are receiving this because you authored the thread.Message ID: @.***>

fcyu commented 9 months ago

No, it is not.

Raghothama1 commented 9 months ago

Reattached Thank you Raghothama

On Tue, Oct 3, 2023 at 3:02 PM Fengchao @.***> wrote:

No, it is not.

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/1269#issuecomment-1745554069, or unsubscribe https://github.com/notifications/unsubscribe-auth/BC6ZSXMRQYUSEMY7RE4DCLTX5ROLZAVCNFSM6AAAAAA5OKMYQCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONBVGU2TIMBWHE . You are receiving this because you authored the thread.Message ID: @.***>

fcyu commented 9 months ago

Still not. Can you click https://github.com/Nesvilab/FragPipe/issues/1269, login, and then reply the message by upload the zipped file?

Thanks,

Fengchao

Raghothama1 commented 9 months ago

log_2023-10-03_13-36-21.zip

fcyu commented 9 months ago

Thanks for your file. Same error as previously mentioned: Process 'Percolator' finished, exit code: -1073741819. Could you remove 20230930_deplPlasma-DIA_120min_1028_1128_1 and try again?

Thanks,

Fengchao

Raghothama1 commented 9 months ago

This time it partially worked. I could see the protein peptide information but there is still some issue. Thank you Raghothama DIA_MS_120min_2-2da-FP_IInd_try.zip

fcyu commented 9 months ago

Could you upgrade EasyPQP to the latest version and try again? You can click the Install/Upgrade EasyPQP in the Config tab, and then wait a few seconds.

Best,

Fengchao

fcyu commented 9 months ago

Also, I see that you were using the raw file. Then, you have to make sure that the correct version of Thermo library is installed because the DIA-NN quant requires that: https://github.com/vdemichev/DiaNN#raw-data-formats

Best,

Fengchao

Raghothama1 commented 8 months ago

I have used the correct version of Thermo library now (3.0v). I am still getting error messages and data analysis is partial. I have attached the logfile here. In my searches there are only DIA files no DDA files. Will it be an issue for DIA library construction? Thank you for your support. Raghothama log_2023-10-07_20-09-28.zip

fcyu commented 8 months ago

Same issue as: https://github.com/Nesvilab/FragPipe/issues/1275. Could you uninstall and install the fixed EasyPQP following the instruction in https://github.com/Nesvilab/FragPipe/issues/1275#issuecomment-1749369666 ?

Thanks,

Fengchao

Raghothama1 commented 8 months ago

log_2023-10-09_14-02-01.zip Still, it cancelled some tasks. I am not sure whether it worked.

EasyPQP is installed properly: Installed Git, and added the path C:\Program Files\Git\bin In cmd, pip install git+https://github.com/Nesvilab/easypqp.git@master

Thanks Raghothama

fcyu commented 8 months ago

No, you did not uninstall and install the EasyPQP correctly. Please following the command in the link I previously mentioned: https://github.com/Nesvilab/FragPipe/issues/1275#issuecomment-1749369666

pip uninstall easypqp -y pip install git+https://github.com/Nesvilab/easypqp.git@master

Best,

Fengchao

Raghothama1 commented 8 months ago

Thank you for the instructions. Now I installed the EasyPQP correctly. Issue is resolved and searches completed without error. Appreciate your help. -Raghothama

Nesvilab / FragPipe

Zero ID crashes Percolator: exit code: -1073741819 #1269