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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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There were issues when load the Thermo raw files. #1340

Closed TimKarr closed 8 months ago

TimKarr commented 8 months ago

Fragpipe sometimes works, sometimes stops with "panic" and "this is a bug" statements. Also, apologies, but Chrome would not allow zip file upload, nor copy/paste of zip file. Original text of the end of the log is below.

G:\100tissues\100tissues_ND\ND_lymph95_15-46.raw: Scans = 0 G:\100tissues\100tissues_ND\ND_cortex1_12-16.raw: Scans = 0 Nov 19, 2023 12:37:04 PM io.grpc.internal.ManagedChannelImpl$2 uncaughtException SEVERE: [Channel<60>: (localhost:54328)] Uncaught exception in the SynchronizationContext. Panic! java.util.concurrent.RejectedExecutionException: event executor terminated at io.grpc.netty.shaded.io.netty.util.concurrent.SingleThreadEventExecutor.reject(SingleThreadEventExecutor.java:934) at io.grpc.netty.shaded.io.netty.util.concurrent.SingleThreadEventExecutor.offerTask(SingleThreadEventExecutor.java:351) at io.grpc.netty.shaded.io.netty.util.concurrent.SingleThreadEventExecutor.addTask(SingleThreadEventExecutor.java:344) at io.grpc.netty.shaded.io.netty.util.concurrent.SingleThreadEventExecutor.execute(SingleThreadEventExecutor.java:836) at io.grpc.netty.shaded.io.netty.util.concurrent.SingleThreadEventExecutor.lazyExecute0(SingleThreadEventExecutor.java:831) at io.grpc.netty.shaded.io.netty.util.concurrent.SingleThreadEventExecutor.lazyExecute(SingleThreadEventExecutor.java:822) at io.grpc.netty.shaded.io.netty.util.concurrent.AbstractScheduledEventExecutor.schedule(AbstractScheduledEventExecutor.java:292) at io.grpc.netty.shaded.io.netty.util.concurrent.AbstractScheduledEventExecutor.schedule(AbstractScheduledEventExecutor.java:205) at io.grpc.netty.shaded.io.netty.util.concurrent.AbstractEventExecutorGroup.schedule(AbstractEventExecutorGroup.java:50) at io.grpc.netty.shaded.io.netty.util.concurrent.AbstractEventExecutorGroup.schedule(AbstractEventExecutorGroup.java:32) at io.grpc.internal.Rescheduler.reschedule(Rescheduler.java:63) at io.grpc.internal.ManagedChannelImpl.rescheduleIdleTimer(ManagedChannelImpl.java:450) at io.grpc.internal.ManagedChannelImpl.exitIdleMode(ManagedChannelImpl.java:405) at io.grpc.internal.ManagedChannelImpl$RealChannel$2.run(ManagedChannelImpl.java:981) at io.grpc.SynchronizationContext.drain(SynchronizationContext.java:95) at io.grpc.SynchronizationContext.execute(SynchronizationContext.java:127) at io.grpc.internal.ManagedChannelImpl$RealChannel.newCall(ManagedChannelImpl.java:978) at io.grpc.internal.ManagedChannelImpl.newCall(ManagedChannelImpl.java:920) at io.grpc.internal.ForwardingManagedChannel.newCall(ForwardingManagedChannel.java:63) at io.grpc.stub.ClientCalls.blockingUnaryCall(ClientCalls.java:150) at com.dmtavt.batmass.io.ms.api.ISourceFactoryGrpc$ISourceFactoryBlockingStub.check(ISourceFactoryGrpc.java:359) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.init(ThermoRawFile.java:226) at umich.ms.fileio.filetypes.thermo.ThermoRawFile.(ThermoRawFile.java:164) at edu.umich.andykong.msfragger.MSFragger.a(Unknown Source) at java.base/java.util.concurrent.FutureTask.run(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source)

Failed in checking G:\100tissues\100tissues_ND\ND_lymph96_15-78.raw. Will ignore it. INTERNAL: Panic! This is a bug! G:\100tissues\100tissues_ND\ND_lymph96_15-78.raw: Scans = 0 [pool-1-thread-3] WARN umich.ms.fileio.filetypes.thermo.ThermoRawFile - Could not shut down communication channel within 5 sec. G:\100tissues\100tissues_ND\ND_kidney20_18-17.raw: Scans = 0 Nov 19, 2023 12:37:25 PM io.grpc.internal.ManagedChannelOrphanWrapper$ManagedChannelReference cleanQueue SEVERE: ~~~ Previous channel ManagedChannelImpl{logId=60, target=localhost:54328} was not shutdown properly!!! ~~~ Make sure to call shutdown()/shutdownNow() and wait until awaitTermination() returns true. G:\100tissues\100tissues_ND\ND_cortex8_14-30.raw: Scans = 86460 G:\100tissues\100tissues_ND\ND_lymph90_14-30.raw: Scans = 90939

fcyu commented 8 months ago

Something was wrong when loading the raw files using the Thermo library. Please convert your files to mzML format and try again: https://fragpipe.nesvilab.org/docs/tutorial_convert.html

Best,

Fengchao

TimKarr commented 8 months ago

Thank you Fengchao, I have also failed to get the mzML converted files to work. Have successfully used other large .RAW files in LFQ mode, unsure what is wrong with these files. I will re-run mzML files again as I neglected to save the log file to compare errors. Very pleased when Fragpipe runs (successfully) and with Analyst, it is GREAT!

Thank you for your help!

Tim

-- Timothy L. Karr, PhD ASU-Banner Neurodegenerative Disease Research Center Assistant Director, KE Operations Manager, Biosciences Mass Spec/Proteomics Core Associate Research Professor, Biodesign Institute Associate Editor, Molecular and Cellular Proteomics https://cores.research.asu.edu/mass-spec/about @.***

From: Fengchao @.> Sent: Sunday, November 19, 2023 2:00 PM To: Nesvilab/FragPipe @.> Cc: Timothy Karr @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] panic and bug issue in java? (Issue #1340)

Something was wrong when loading the raw files using the Thermo library. Please convert your files to mzML format and try again: https://fragpipe.nesvilab.org/docs/tutorial_convert.htmlhttps://urldefense.com/v3/__https:/fragpipe.nesvilab.org/docs/tutorial_convert.html__;!!IKRxdwAv5BmarQ!bPuu33zgly9qnRnlu2ksa_4gA6Fwc_imYb2GV-GdVuPHJw_koZ97sd2rB5llObRgDmXee0aduuOhnd2503CuIQ$

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/Nesvilab/FragPipe/issues/1340*issuecomment-1817975905__;Iw!!IKRxdwAv5BmarQ!bPuu33zgly9qnRnlu2ksa_4gA6Fwc_imYb2GV-GdVuPHJw_koZ97sd2rB5llObRgDmXee0aduuOhnd3w2_UEjw$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/APOK4XGASIAVJQ3CTTO4DL3YFJXMHAVCNFSM6AAAAAA7R7UVIWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJXHE3TKOJQGU__;!!IKRxdwAv5BmarQ!bPuu33zgly9qnRnlu2ksa_4gA6Fwc_imYb2GV-GdVuPHJw_koZ97sd2rB5llObRgDmXee0aduuOhnd1PVRXUTA$. You are receiving this because you authored the thread.Message ID: @.**@.>>

fcyu commented 8 months ago

I have also failed to get the mzML converted files to work.

If msconvert can't convert the raw files to mzML, then very like the raw files were corrupted.

Best,

Fengchao

TimKarr commented 8 months ago

Sorry for the confusion Fengchao, MSConvert successfully converted the files and were loaded into FP…, but did not finish with similar errors reported. This has happened before, even with the files that did work previously (from a different experiment but still RAW files were loaded). I moved the files to the local C drive and this seemed to fix the problem but have not systematically confirmed this…, will copy these offending files to the C drive and try again. It really is quite odd to this non-coding and non-expert 😊.

Thanks again, Tim

-- Timothy L. Karr, PhD ASU-Banner Neurodegenerative Disease Research Center Assistant Director, KE Operations Manager, Biosciences Mass Spec/Proteomics Core Associate Research Professor, Biodesign Institute Associate Editor, Molecular and Cellular Proteomics https://cores.research.asu.edu/mass-spec/about @.***

From: Fengchao @.> Sent: Sunday, November 19, 2023 2:09 PM To: Nesvilab/FragPipe @.> Cc: Timothy Karr @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] There were issues when load the Thermo raw files. (Issue #1340)

I have also failed to get the mzML converted files to work.

If msconvert can't convert the raw files to mzML, then very like the raw files were corrupted.

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/Nesvilab/FragPipe/issues/1340*issuecomment-1817977976__;Iw!!IKRxdwAv5BmarQ!akBMBRFbwaw6N0rMZ5uthLY3vjsr1xqLam-a1_V0tf2YJNwdmHjCaegO3UO1A1sV2gfypyLYui0rTtNSkxJffQ$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/APOK4XFF4XLRYMCLUNNKVADYFJYN5AVCNFSM6AAAAAA7R7UVIWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJXHE3TOOJXGY__;!!IKRxdwAv5BmarQ!akBMBRFbwaw6N0rMZ5uthLY3vjsr1xqLam-a1_V0tf2YJNwdmHjCaegO3UO1A1sV2gfypyLYui0rTtM6k5KVDQ$. You are receiving this because you authored the thread.Message ID: @.**@.>>

fcyu commented 8 months ago

Hi Tim,

Yeah, it sounds weird. If you still have the log files, could you upload them here https://github.com/Nesvilab/FragPipe/issues/1340 ?

Thanks,

Fengchao

TimKarr commented 8 months ago

Dear Fengchao,

1340 looks like it is closed so have copied two log files that are perplexing: The first completed as expected using 9 RAW files and the “default” workflow, (named #1), but (#2) using the same 9 files and the “LFQ-MBR” failed with error message (“There are corrupted files. Please remove those files and re-start the task.”). This consistently happens with other files in this rather large dataset when attempting to run the LFQ workflow. BTW, all these files have been successfully processed with Proteome Discoverer 2.5, which is even more confusing. I really wish to use Fragpipe but am stymied at this point, hope you can provide some guidance.

Kind regards, Tim

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Logs from Fragpipe +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ (#1) System OS: Windows 10, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK .NET Core Info: 6.0.14

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

LCMS files: Experiment/Group: cortex_1

108 commands to execute: CheckCentroid C:\fragpipe\jre\bin\java.exe -Xmx5G -cp "C:\fragpipe\lib\fragpipe-20.0.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid G:\100tissues\13X_ADtissues\AD_cortex2_12-27.raw 7 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\c29aacb2-8b83-4e7a-97e3-fdb3e3366f9c WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\df8affd1-4b3c-4756-a039-028053a9e40f WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\005ba5ac-f2c1-40cc-9580-74392bc78a8b WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\c94586cd-b69a-4ce8-a608-dc8e761dbb3b WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\b3bb9d6a-ca81-47f3-b97f-099119cf486e WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidney_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidney_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\38c81ea7-b5c3-4572-94b7-d31493c86b74 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\05f1fbe4-758f-4a80-9b74-a47d7ce35b52 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidey_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidey_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\751db5a8-a28a-4ef0-a59c-c1644faf947b WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidney_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidney_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\2f2a5b63-a1ca-42b6-b31f-e7c6ee62115a WorkspaceCleanInit [Work dir: C:\fragpipe\folder4] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\fragpipe\folder4] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\7a03a7d4-c0aa-46af-af30-827cd8b53051 MSFragger [Work dir: C:\fragpipe\folder4] C:\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx5G C:\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar C:\fragpipe\folder4\fragger.params G:\100tissues\13X_ADtissues\AD_cortex2_12-27.raw G:\100tissues\13X_ADtissues\AD_cortex3_13-31.raw G:\100tissues\13X_ADtissues\AD_cortex4_13-42.raw G:\100tissues\13X_ADtissues\AD_kidney23_13-31.raw G:\100tissues\13X_ADtissues\AD_kidney22_12-27.raw G:\100tissues\13X_ADtissues\AD_kidney24_13-42.raw G:\100tissues\13X_ADtissues\AD_liver43_13-31.raw G:\100tissues\13X_ADtissues\AD_liver44_13-42.raw G:\100tissues\13X_ADtissues\AD_liver45_13-66.raw MSFragger move pepxml C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_cortex2_12-27.pepXML C:\fragpipe\folder4\cortex_1\AD_cortex2_12-27.pepXML MSFragger move pin C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_cortex2_12-27.pin C:\fragpipe\folder4\cortex_1\AD_cortex2_12-27.pin MSFragger move pepxml C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_cortex3_13-31.pepXML C:\fragpipe\folder4\cortex_2\AD_cortex3_13-31.pepXML MSFragger move pin C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_cortex3_13-31.pin C:\fragpipe\folder4\cortex_2\AD_cortex3_13-31.pin MSFragger move pepxml C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_cortex4_13-42.pepXML C:\fragpipe\folder4\cortex_3\AD_cortex4_13-42.pepXML MSFragger move pin C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_cortex4_13-42.pin C:\fragpipe\folder4\cortex_3\AD_cortex4_13-42.pin MSFragger move pepxml C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_kidney23_13-31.pepXML C:\fragpipe\folder4\kidey_2\AD_kidney23_13-31.pepXML MSFragger move pin C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_kidney23_13-31.pin C:\fragpipe\folder4\kidey_2\AD_kidney23_13-31.pin MSFragger move pepxml C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_kidney22_12-27.pepXML C:\fragpipe\folder4\kidney_1\AD_kidney22_12-27.pepXML MSFragger move pin C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_kidney22_12-27.pin C:\fragpipe\folder4\kidney_1\AD_kidney22_12-27.pin MSFragger move pepxml C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_kidney24_13-42.pepXML C:\fragpipe\folder4\kidney_3\AD_kidney24_13-42.pepXML MSFragger move pin C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_kidney24_13-42.pin C:\fragpipe\folder4\kidney_3\AD_kidney24_13-42.pin MSFragger move pepxml C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_liver43_13-31.pepXML C:\fragpipe\folder4\liver_1\AD_liver43_13-31.pepXML MSFragger move pin C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_liver43_13-31.pin C:\fragpipe\folder4\liver_1\AD_liver43_13-31.pin MSFragger move pepxml C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_liver44_13-42.pepXML C:\fragpipe\folder4\liver_2\AD_liver44_13-42.pepXML MSFragger move pin C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_liver44_13-42.pin C:\fragpipe\folder4\liver_2\AD_liver44_13-42.pin MSFragger move pepxml C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_liver45_13-66.pepXML C:\fragpipe\folder4\liver_3\AD_liver45_13-66.pepXML MSFragger move pin C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar;/C:/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err G:\100tissues\13X_ADtissues\AD_liver45_13-66.pin C:\fragpipe\folder4\liver_3\AD_liver45_13-66.pin MSBooster [Work dir: C:\fragpipe\folder4] C:\fragpipe\jre\bin\java.exe -Xmx5G -cp "C:\fragpipe\tools\msbooster-1.1.11.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" Features.MainClass --paramsList C:\fragpipe\folder4\msbooster_params.txt Percolator [Work dir: C:\fragpipe\folder4\liver_1] C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms AD_liver43_13-31_percolator_target_psms.tsv --decoy-results-psms AD_liver43_13-31_percolator_decoypsms.tsv --protein-decoy-pattern rev AD_liver43_13-31_edited.pin Percolator [Work dir: C:\fragpipe\folder4\liver_3] C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms AD_liver45_13-66_percolator_target_psms.tsv --decoy-results-psms AD_liver45_13-66_percolator_decoypsms.tsv --protein-decoy-pattern rev AD_liver45_13-66_edited.pin Percolator [Work dir: C:\fragpipe\folder4\cortex_3] C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms AD_cortex4_13-42_percolator_target_psms.tsv --decoy-results-psms AD_cortex4_13-42_percolator_decoypsms.tsv --protein-decoy-pattern rev AD_cortex4_13-42_edited.pin Percolator [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms AD_cortex2_12-27_percolator_target_psms.tsv --decoy-results-psms AD_cortex2_12-27_percolator_decoypsms.tsv --protein-decoy-pattern rev AD_cortex2_12-27_edited.pin Percolator [Work dir: C:\fragpipe\folder4\cortex_2] C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms AD_cortex3_13-31_percolator_target_psms.tsv --decoy-results-psms AD_cortex3_13-31_percolator_decoypsms.tsv --protein-decoy-pattern rev AD_cortex3_13-31_edited.pin Percolator [Work dir: C:\fragpipe\folder4\liver_2] C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms AD_liver44_13-42_percolator_target_psms.tsv --decoy-results-psms AD_liver44_13-42_percolator_decoypsms.tsv --protein-decoy-pattern rev AD_liver44_13-42_edited.pin Percolator [Work dir: C:\fragpipe\folder4\kidney_3] C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms AD_kidney24_13-42_percolator_target_psms.tsv --decoy-results-psms AD_kidney24_13-42_percolator_decoypsms.tsv --protein-decoy-pattern rev AD_kidney24_13-42_edited.pin Percolator [Work dir: C:\fragpipe\folder4\kidey_2] C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms AD_kidney23_13-31_percolator_target_psms.tsv --decoy-results-psms AD_kidney23_13-31_percolator_decoypsms.tsv --protein-decoy-pattern rev AD_kidney23_13-31_edited.pin Percolator [Work dir: C:\fragpipe\folder4\kidney_1] C:\fragpipe\tools\percolator-306\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 7 --results-psms AD_kidney22_12-27_percolator_target_psms.tsv --decoy-results-psms AD_kidney22_12-27_percolator_decoypsms.tsv --protein-decoy-pattern rev AD_kidney22_12-27_edited.pin Percolator: Convert to pepxml [Work dir: C:\fragpipe\folder4\liver_1] C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AD_liver43_13-31.pin AD_liver43_13-31 AD_liver43_13-31_percolator_target_psms.tsv AD_liver43_13-31_percolator_decoy_psms.tsv interact-AD_liver43_13-31 DDA 0.5 G:\100tissues\13X_ADtissues\AD_liver43_13-31_uncalibrated.mzML Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\liver_1\AD_liver43_13-31_percolator_target_psms.tsv Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\liver_1\AD_liver43_13-31_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\fragpipe\folder4\liver_3] C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AD_liver45_13-66.pin AD_liver45_13-66 AD_liver45_13-66_percolator_target_psms.tsv AD_liver45_13-66_percolator_decoy_psms.tsv interact-AD_liver45_13-66 DDA 0.5 G:\100tissues\13X_ADtissues\AD_liver45_13-66_uncalibrated.mzML Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\liver_3\AD_liver45_13-66_percolator_target_psms.tsv Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\liver_3\AD_liver45_13-66_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\fragpipe\folder4\cortex_3] C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AD_cortex4_13-42.pin AD_cortex4_13-42 AD_cortex4_13-42_percolator_target_psms.tsv AD_cortex4_13-42_percolator_decoy_psms.tsv interact-AD_cortex4_13-42 DDA 0.5 G:\100tissues\13X_ADtissues\AD_cortex4_13-42_uncalibrated.mzML Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\cortex_3\AD_cortex4_13-42_percolator_target_psms.tsv Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\cortex_3\AD_cortex4_13-42_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AD_cortex2_12-27.pin AD_cortex2_12-27 AD_cortex2_12-27_percolator_target_psms.tsv AD_cortex2_12-27_percolator_decoy_psms.tsv interact-AD_cortex2_12-27 DDA 0.5 G:\100tissues\13X_ADtissues\AD_cortex2_12-27_uncalibrated.mzML Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\cortex_1\AD_cortex2_12-27_percolator_target_psms.tsv Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\cortex_1\AD_cortex2_12-27_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\fragpipe\folder4\cortex_2] C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AD_cortex3_13-31.pin AD_cortex3_13-31 AD_cortex3_13-31_percolator_target_psms.tsv AD_cortex3_13-31_percolator_decoy_psms.tsv interact-AD_cortex3_13-31 DDA 0.5 G:\100tissues\13X_ADtissues\AD_cortex3_13-31_uncalibrated.mzML Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\cortex_2\AD_cortex3_13-31_percolator_target_psms.tsv Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\cortex_2\AD_cortex3_13-31_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\fragpipe\folder4\liver_2] C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AD_liver44_13-42.pin AD_liver44_13-42 AD_liver44_13-42_percolator_target_psms.tsv AD_liver44_13-42_percolator_decoy_psms.tsv interact-AD_liver44_13-42 DDA 0.5 G:\100tissues\13X_ADtissues\AD_liver44_13-42_uncalibrated.mzML Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\liver_2\AD_liver44_13-42_percolator_target_psms.tsv Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\liver_2\AD_liver44_13-42_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\fragpipe\folder4\kidney_3] C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AD_kidney24_13-42.pin AD_kidney24_13-42 AD_kidney24_13-42_percolator_target_psms.tsv AD_kidney24_13-42_percolator_decoy_psms.tsv interact-AD_kidney24_13-42 DDA 0.5 G:\100tissues\13X_ADtissues\AD_kidney24_13-42_uncalibrated.mzML Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\kidney_3\AD_kidney24_13-42_percolator_target_psms.tsv Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\kidney_3\AD_kidney24_13-42_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\fragpipe\folder4\kidey_2] C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AD_kidney23_13-31.pin AD_kidney23_13-31 AD_kidney23_13-31_percolator_target_psms.tsv AD_kidney23_13-31_percolator_decoy_psms.tsv interact-AD_kidney23_13-31 DDA 0.5 G:\100tissues\13X_ADtissues\AD_kidney23_13-31_uncalibrated.mzML Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\kidey_2\AD_kidney23_13-31_percolator_target_psms.tsv Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\kidey_2\AD_kidney23_13-31_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: C:\fragpipe\folder4\kidney_1] C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib/* com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML AD_kidney22_12-27.pin AD_kidney22_12-27 AD_kidney22_12-27_percolator_target_psms.tsv AD_kidney22_12-27_percolator_decoy_psms.tsv interact-AD_kidney22_12-27 DDA 0.5 G:\100tissues\13X_ADtissues\AD_kidney22_12-27_uncalibrated.mzML Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\kidney_1\AD_kidney22_12-27_percolator_target_psms.tsv Percolator: Delete temp C:\fragpipe\jre\bin\java.exe -cp C:\fragpipe\lib\fragpipe-20.0.jar com.github.chhh.utils.FileDelete C:\fragpipe\folder4\kidney_1\AD_kidney22_12-27_percolator_decoy_psms.tsv ProteinProphet [Work dir: C:\fragpipe\folder4] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe proteinprophet --maxppmdiff 2000000 --output combined C:\fragpipe\folder4\filelist_proteinprophet.txt PhilosopherDbAnnotate [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe database --annotate C:\fragpipe\2023-11-17-decoys-reviewed-contam-UP000005640.fas --prefix rev PhilosopherFilter [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml C:\fragpipe\folder4\cortex_1 --protxml C:\fragpipe\folder4\combined.prot.xml --razor PhilosopherFilter [Work dir: C:\fragpipe\folder4\cortex_2] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml C:\fragpipe\folder4\cortex_2 --protxml C:\fragpipe\folder4\combined.prot.xml --probin C:\fragpipe\folder4\cortex_1 --razor PhilosopherFilter [Work dir: C:\fragpipe\folder4\cortex_3] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml C:\fragpipe\folder4\cortex_3 --protxml C:\fragpipe\folder4\combined.prot.xml --probin C:\fragpipe\folder4\cortex_1 --razor PhilosopherFilter [Work dir: C:\fragpipe\folder4\kidey_2] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml C:\fragpipe\folder4\kidey_2 --protxml C:\fragpipe\folder4\combined.prot.xml --probin C:\fragpipe\folder4\cortex_1 --razor PhilosopherFilter [Work dir: C:\fragpipe\folder4\kidney_1] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml C:\fragpipe\folder4\kidney_1 --protxml C:\fragpipe\folder4\combined.prot.xml --probin C:\fragpipe\folder4\cortex_1 --razor PhilosopherFilter [Work dir: C:\fragpipe\folder4\kidney_3] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml C:\fragpipe\folder4\kidney_3 --protxml C:\fragpipe\folder4\combined.prot.xml --probin C:\fragpipe\folder4\cortex_1 --razor PhilosopherFilter [Work dir: C:\fragpipe\folder4\liver_1] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml C:\fragpipe\folder4\liver_1 --protxml C:\fragpipe\folder4\combined.prot.xml --probin C:\fragpipe\folder4\cortex_1 --razor PhilosopherFilter [Work dir: C:\fragpipe\folder4\liver_2] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml C:\fragpipe\folder4\liver_2 --protxml C:\fragpipe\folder4\combined.prot.xml --probin C:\fragpipe\folder4\cortex_1 --razor PhilosopherFilter [Work dir: C:\fragpipe\folder4\liver_3] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe filter --sequential --picked --prot 0.01 --tag rev --pepxml C:\fragpipe\folder4\liver_3 --protxml C:\fragpipe\folder4\combined.prot.xml --probin C:\fragpipe\folder4\cortex_1 --razor PhilosopherReport [Work dir: C:\fragpipe\folder4\liver_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: C:\fragpipe\folder4\liver_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: C:\fragpipe\folder4\liver_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: C:\fragpipe\folder4\cortex_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: C:\fragpipe\folder4\cortex_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: C:\fragpipe\folder4\kidney_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: C:\fragpipe\folder4\kidey_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PhilosopherReport [Work dir: C:\fragpipe\folder4\kidney_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe report PhilosopherAbacus [Work dir: C:\fragpipe\folder4] C:\fragpipe\tools\philosopher_v5.0.0_windowsamd64\philosopher.exe abacus --picked --razor --reprint --tag rev --protein cortex_1 cortex_2 cortex_3 kidey_2 kidney_1 kidney_3 liver_1 liver_2 liver_3 WorkspaceClean [Work dir: C:\fragpipe\folder4\liver_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\fragpipe\folder4\liver_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\fragpipe\folder4\liver_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\fragpipe\folder4\cortex_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\fragpipe\folder4\cortex_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\fragpipe\folder4\kidney_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\fragpipe\folder4\kidey_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\fragpipe\folder4\kidney_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceClean [Work dir: C:\fragpipe\folder4] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck


Execution order:

    Cmd: [START], Work dir: [C:\fragpipe\folder4]
    Cmd: [CheckCentroid], Work dir: [C:\fragpipe\folder4]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4\liver_3]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4\liver_2]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4\liver_1]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4\cortex_3]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4\cortex_2]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4\kidney_3]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4\cortex_1]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4\kidey_2]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4\kidney_1]
    Cmd: [WorkspaceCleanInit], Work dir: [C:\fragpipe\folder4]
    Cmd: [MSFragger], Work dir: [C:\fragpipe\folder4]
    Cmd: [MSBooster], Work dir: [C:\fragpipe\folder4]
    Cmd: [Percolator], Work dir: [C:\fragpipe\folder4]
    Cmd: [ProteinProphet], Work dir: [C:\fragpipe\folder4]
    Cmd: [PhilosopherDbAnnotate], Work dir: [C:\fragpipe\folder4]
    Cmd: [PhilosopherFilter], Work dir: [C:\fragpipe\folder4]
    Cmd: [PhilosopherReport], Work dir: [C:\fragpipe\folder4]
    Cmd: [PhilosopherAbacus], Work dir: [C:\fragpipe\folder4]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4\liver_3]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4\liver_2]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4\liver_1]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4\cortex_3]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4\cortex_2]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4\kidney_3]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4\cortex_1]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4\kidey_2]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4\kidney_1]
    Cmd: [WorkspaceClean], Work dir: [C:\fragpipe\folder4]

>contam_sp|O77727|K1C15_SHEEP Keratin, type I cytoskeletal 15 OS=Ovis aries OX=9940 GN=KRT15 PE=2 SV=1
>rev_sp|O43513|MED7_HUMAN Mediator of RNA polymerase II transcription subunit 7 OS=Homo sapiens OX=9606 GN=MED7 PE=1 SV=1
>rev_sp|P0DMN0|ST1A4_HUMAN Sulfotransferase 1A4 OS=Homo sapiens OX=9606 GN=SULT1A4 PE=1 SV=1
>rev_sp|P49711|CTCF_HUMAN Transcriptional repressor CTCF OS=Homo sapiens OX=9606 GN=CTCF PE=1 SV=1
>rev_sp|Q14154|DELE1_HUMAN DAP3-binding cell death enhancer 1 OS=Homo sapiens OX=9606 GN=DELE1 PE=1 SV=3
>rev_sp|Q68DV7|RNF43_HUMAN E3 ubiquitin-protein ligase RNF43 OS=Homo sapiens OX=9606 GN=RNF43 PE=1 SV=1
>rev_sp|Q8IWE5|PKHM2_HUMAN Pleckstrin homology domain-containing family M member 2 OS=Homo sapiens OX=9606 GN=PLEKHM2 PE=1 SV=2
>rev_sp|Q8WVM0|TFB1M_HUMAN Dimethyladenosine transferase 1, mitochondrial OS=Homo sapiens OX=9606 GN=TFB1M PE=1 SV=1
>rev_sp|Q9BRI3|ZNT2_HUMAN Proton-coupled zinc antiporter SLC30A2 OS=Homo sapiens OX=9606 GN=SLC30A2 PE=1 SV=2
>rev_sp|Q9NUQ8|ABCF3_HUMAN ATP-binding cassette sub-family F member 3 OS=Homo sapiens OX=9606 GN=ABCF3 PE=1 SV=2
>rev_sp|Q9Y6N9|USH1C_HUMAN Harmonin OS=Homo sapiens OX=9606 GN=USH1C PE=1 SV=3
>sp|O43674|NDUB5_HUMAN NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFB5 PE=1 SV=1
>sp|P0DP08|HVD82_HUMAN Immunoglobulin heavy variable 4-38-2 OS=Homo sapiens OX=9606 GN=IGHV4-38-2 PE=3 SV=1
>sp|P49903|SPS1_HUMAN Selenide, water dikinase 1 OS=Homo sapiens OX=9606 GN=SEPHS1 PE=1 SV=2
>sp|Q14296|FASTK_HUMAN Fas-activated serine/threonine kinase OS=Homo sapiens OX=9606 GN=FASTK PE=1 SV=1
>sp|Q6BCY4|NB5R2_HUMAN NADH-cytochrome b5 reductase 2 OS=Homo sapiens OX=9606 GN=CYB5R2 PE=1 SV=1
>sp|Q8IX03|KIBRA_HUMAN Protein KIBRA OS=Homo sapiens OX=9606 GN=WWC1 PE=1 SV=1
>sp|Q8WWF8|CAPSL_HUMAN Calcyphosin-like protein OS=Homo sapiens OX=9606 GN=CAPSL PE=2 SV=4
>sp|Q9BS18|APC13_HUMAN Anaphase-promoting complex subunit 13 OS=Homo sapiens OX=9606 GN=ANAPC13 PE=1 SV=1
>sp|Q9NVI1|FANCI_HUMAN Fanconi anemia group I protein OS=Homo sapiens OX=9606 GN=FANCI PE=1 SV=4
>sp|X6R8D5|CMIP3_HUMAN Putative uncharacterized protein CIMIP3 OS=Homo sapiens OX=9606 GN=CIMIP3 PE=5 SV=2
# 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\:\\fragpipe\\2023-11-17-decoys-reviewed-contam-UP000005640.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=false
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=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=C\:\\fragpipe\\tools\\IonQuant-1.9.8.jar
fragpipe-config.bin-msfragger=C\:\\fragpipe\\tools\\MSFragger-3.8\\MSFragger-3.8.jar
fragpipe-config.bin-philosopher=C\:\\fragpipe\\tools\\philosopher_v5.0.0_windows_amd64\\philosopher.exe
fragpipe-config.bin-python=C\:\\ProgramData\\anaconda3\\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=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.group_variable=0
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2/3
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.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; 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.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=0.5
percolator.run-percolator=true
phi-report.dont-use-prot-proph-file=false
phi-report.filter=--sequential --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
protein-prophet.run-protein-prophet=true
ptmprophet.cmdline=KEEPOLD STATIC EM\=1 NIONS\=b M\:15.9949,n\:42.0106 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=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=ciRT
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
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\:\\fragpipe\\folder4
workflow.input.data-type.im-ms=false
workflow.input.data-type.regular-ms=true
workflow.ram=0
workflow.threads=7

CheckCentroid C:\fragpipe\jre\bin\java.exe -Xmx5G -cp "C:\fragpipe\lib\fragpipe-20.0.jar;C:\fragpipe\tools\batmass-io-1.28.12.jar" com.dmtavt.fragpipe.util.CheckCentroid G:\100tissues\13X_ADtissues\AD_cortex2_12-27.raw 7 Done in 0.0 s. Process 'CheckCentroid' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:04] Executing Workspace v5.0.0 INFO[21:10:04] Removing workspace WARN[21:10:04] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:04] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\c29aacb2-8b83-4e7a-97e3-fdb3e3366f9c INFO[21:10:04] Executing Workspace v5.0.0 INFO[21:10:04] Creating workspace INFO[21:10:04] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:04] Executing Workspace v5.0.0 INFO[21:10:04] Removing workspace WARN[21:10:04] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:04] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\df8affd1-4b3c-4756-a039-028053a9e40f INFO[21:10:05] Executing Workspace v5.0.0 INFO[21:10:05] Creating workspace INFO[21:10:05] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:05] Executing Workspace v5.0.0 INFO[21:10:05] Removing workspace WARN[21:10:05] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:05] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\liver_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\005ba5ac-f2c1-40cc-9580-74392bc78a8b INFO[21:10:06] Executing Workspace v5.0.0 INFO[21:10:06] Creating workspace INFO[21:10:06] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:06] Executing Workspace v5.0.0 INFO[21:10:06] Removing workspace WARN[21:10:06] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:06] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\c94586cd-b69a-4ce8-a608-dc8e761dbb3b INFO[21:10:06] Executing Workspace v5.0.0 INFO[21:10:06] Creating workspace INFO[21:10:06] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:07] Executing Workspace v5.0.0 INFO[21:10:07] Removing workspace WARN[21:10:07] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:07] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\b3bb9d6a-ca81-47f3-b97f-099119cf486e INFO[21:10:07] Executing Workspace v5.0.0 INFO[21:10:07] Creating workspace INFO[21:10:07] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidney_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:08] Executing Workspace v5.0.0 INFO[21:10:08] Removing workspace WARN[21:10:08] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:08] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidney_3] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\38c81ea7-b5c3-4572-94b7-d31493c86b74 INFO[21:10:08] Executing Workspace v5.0.0 INFO[21:10:08] Creating workspace INFO[21:10:08] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:09] Executing Workspace v5.0.0 INFO[21:10:09] Removing workspace WARN[21:10:09] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:09] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\cortex_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\05f1fbe4-758f-4a80-9b74-a47d7ce35b52 INFO[21:10:09] Executing Workspace v5.0.0 INFO[21:10:09] Creating workspace INFO[21:10:09] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidey_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:09] Executing Workspace v5.0.0 INFO[21:10:09] Removing workspace WARN[21:10:09] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:09] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidey_2] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\751db5a8-a28a-4ef0-a59c-c1644faf947b INFO[21:10:10] Executing Workspace v5.0.0 INFO[21:10:10] Creating workspace INFO[21:10:10] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidney_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:10] Executing Workspace v5.0.0 INFO[21:10:10] Removing workspace WARN[21:10:10] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:10] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4\kidney_1] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\2f2a5b63-a1ca-42b6-b31f-e7c6ee62115a INFO[21:10:11] Executing Workspace v5.0.0 INFO[21:10:11] Creating workspace INFO[21:10:11] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --clean --nocheck INFO[21:10:11] Executing Workspace v5.0.0 INFO[21:10:11] Removing workspace WARN[21:10:11] Cannot read file. open .meta\meta.bin: The system cannot find the path specified. INFO[21:10:11] Done Process 'WorkspaceCleanInit' finished, exit code: 0 WorkspaceCleanInit [Work dir: C:\fragpipe\folder4] C:\fragpipe\tools\philosopher_v5.0.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\tkarr\AppData\Local\Temp\7a03a7d4-c0aa-46af-af30-827cd8b53051 INFO[21:10:12] Executing Workspace v5.0.0 INFO[21:10:12] Creating workspace INFO[21:10:12] Done Process 'WorkspaceCleanInit' finished, exit code: 0 MSFragger [Work dir: C:\fragpipe\folder4] C:\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx5G C:\fragpipe\tools\MSFragger-3.8\MSFragger-3.8.jar C:\fragpipe\folder4\fragger.params G:\100tissues\13X_ADtissues\AD_cortex2_12-27.raw G:\100tissues\13X_ADtissues\AD_cortex3_13-31.raw G:\100tissues\13X_ADtissues\AD_cortex4_13-42.raw G:\100tissues\13X_ADtissues\AD_kidney23_13-31.raw G:\100tissues\13X_ADtissues\AD_kidney22_12-27.raw G:\100tissues\13X_ADtissues\AD_kidney24_13-42.raw G:\100tissues\13X_ADtissues\AD_liver43_13-31.raw G:\100tissues\13X_ADtissues\AD_liver44_13-42.raw G:\100tissues\13X_ADtissues\AD_liver45_13-66.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 5 GB memory Checking database... Checking spectral files... G:\100tissues\13X_ADtissues\AD_cortex4_13-42.raw: Scans = 86985 G:\100tissues\13X_ADtissues\AD_cortex2_12-27.raw: Scans = 87637 G:\100tissues\13X_ADtissues\AD_kidney24_13-42.raw: Scans = 90319 G:\100tissues\13X_ADtissues\AD_liver44_13-42.raw: Scans = 90865 G:\100tissues\13X_ADtissues\AD_liver43_13-31.raw: Scans = 91200 G:\100tissues\13X_ADtissues\AD_cortex3_13-31.raw: Scans = 88654 G:\100tissues\13X_ADtissues\AD_kidney23_13-31.raw: Scans = 90094 G:\100tissues\13X_ADtissues\AD_kidney22_12-27.raw: Scans = 90265 G:\100tissues\13X_ADtissues\AD_liver45_13-66.raw: Scans = 91560 ***FIRST SEARCH**** Parameters: num_threads = 7 database_name = C:\fragpipe\2023-11-17-decoys-reviewed-contam-UP000005640.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 = 20.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1 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 = 2 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 = 50.0 report_alternative_proteins = 0 override_charge = 0 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 = 150 minIonsScoring = 2 min_matched_fragments = 4 minimum_ratio = 0.01 intensity_transform = 0 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 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 = 1 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 Selected fragment index width 0.10 Da. 323493968 fragments to be searched in 2 slices (4.82 GB total) Operating on slice 1 of 2: Fragment index slice generated in 3.26 s

  1. AD_cortex2_12-27.raw 37.3 s | deisotoping 0.9 s [progress: 86470/86470 (100%) - 14852 spectra/s] 5.8s
  2. AD_cortex3_13-31.raw 28.1 s | deisotoping 0.1 s [progress: 85681/85681 (100%) - 41552 spectra/s] 2.1s
  3. AD_cortex4_13-42.raw 31.8 s | deisotoping 0.1 s [progress: 85295/85295 (100%) - 21561 spectra/s] 4.0s
  4. AD_kidney22_12-27.raw 36.2 s | deisotoping 0.2 s [progress: 89353/89353 (100%) - 16777 spectra/s] 5.3s
  5. AD_kidney23_13-31.raw 38.2 s | deisotoping 0.5 s [progress: 89516/89516 (100%) - 14311 spectra/s] 6.3s
  6. AD_kidney24_13-42.raw 36.9 s | deisotoping 0.4 s [progress: 89579/89579 (100%) - 14903 spectra/s] 6.0s
  7. AD_liver43_13-31.raw 40.1 s | deisotoping 0.7 s [progress: 90390/90390 (100%) - 12041 spectra/s] 7.5s
  8. AD_liver44_13-42.raw 39.6 s | deisotoping 0.7 s [progress: 89919/89919 (100%) - 11224 spectra/s] 8.0s
  9. AD_liver45_13-66.raw 41.5 s | deisotoping 0.8 s [progress: 90658/90658 (100%) - 10753 spectra/s] 8.4s Operating on slice 2 of 2: Fragment index slice generated in 3.05 s
  10. AD_cortex2_12-27.raw 23.7 s | deisotoping 0.2 s [progress: 86470/86470 (100%) - 40846 spectra/s] 2.1s | postprocessing 0.7 s
  11. AD_cortex3_13-31.raw 17.5 s | deisotoping 0.2 s [progress: 85681/85681 (100%) - 59917 spectra/s] 1.4s | postprocessing 0.3 s
  12. AD_cortex4_13-42.raw 19.7 s | deisotoping 0.1 s [progress: 85295/85295 (100%) - 53276 spectra/s] 1.6s | postprocessing 0.5 s
  13. AD_kidney22_12-27.raw 26.7 s | deisotoping 0.4 s [progress: 89353/89353 (100%) - 38169 spectra/s] 2.3s | postprocessing 0.6 s
  14. AD_kidney23_13-31.raw 22.6 s | deisotoping 0.5 s [progress: 89516/89516 (100%) - 31766 spectra/s] 2.8s | postprocessing 0.5 s
  15. AD_kidney24_13-42.raw 22.4 s | deisotoping 0.6 s [progress: 89579/89579 (100%) - 31365 spectra/s] 2.9s | postprocessing 0.5 s
  16. AD_liver43_13-31.raw 24.3 s | deisotoping 0.9 s [progress: 90390/90390 (100%) - 31255 spectra/s] 2.9s | postprocessing 0.5 s
  17. AD_liver44_13-42.raw 24.1 s | deisotoping 0.8 s [progress: 89919/89919 (100%) - 32000 spectra/s] 2.8s | postprocessing 1.2 s
  18. AD_liver45_13-66.raw 25.5 s | deisotoping 1.0 s [progress: 90658/90658 (100%) - 29273 spectra/s] 3.1s | postprocessing 0.6 s ***FIRST SEARCH DONE IN 11.572 MIN**
**MASS CALIBRATION AND PARAMETER OPTIMIZATION ----- --------------- --------------- --------------- --------------- MS1 (Old) MS1 (New) MS2 (Old) MS2 (New)
Run Median MAD Median MAD Median MAD Median MAD
001 5.48 0.70 0.02 0.50 7.12 1.63 -0.10 1.51
002 5.11 0.85 -0.05 0.56 6.57 1.69 -0.13 1.59
003 4.51 0.60 0.03 0.45 6.17 1.57 -0.17 1.45
004 4.78 0.87 -0.01 0.64 6.40 1.61 -0.04 1.46
005 5.12 0.67 0.02 0.52 7.29 1.56 -0.05 1.36
006 5.28 0.75 0.03 0.57 7.04 1.57 -0.02 1.39
007 4.53 0.83 0.04 0.60 6.48 1.51 -0.05 1.33
008 4.44 0.85 0.00 0.58 6.40 1.53 -0.07 1.32
009 4.78 0.74 -0.00 0.56 6.92 1.51 -0.03 1.32
----- --------------- --------------- --------------- ---------------
Finding the optimal parameters: ------- ------- ------- ------- ------- ------- ------- ------- ------- MS2 5 7 10 15 20 25 30 50
Count 47308 47662 48385 47957 skip rest
------- ------- ------- ------- ------- ------- ------- ------- -------
------- ------- ------- ------- ------- ------- -------
Peaks 300_0 200_0 175_0 150_1 125_1 100_1
------- ------- ------- ------- ------- ------- -------
Count 49195 49122 skip rest
------- ------- ------- ------- ------- ------- -------
------- -------
Int. 1
------- -------
Count 49828
------- -------
------- -------
Rm P. 0
------- -------
Count 49850
------- -------

New fragment_mass_tolerance = 10 PPM New use_topN_peaks = 300 New minimum_ratio = 0.000000 New intensity_transform = 1 New remove_precursor_peak = 0 ****MASS CALIBRATION AND PARAMETER OPTIMIZATION DONE IN 7.157 MIN*****

****MAIN SEARCH**** Checking database... Parameters: num_threads = 7 database_name = C:\fragpipe\2023-11-17-decoys-reviewed-contam-UP000005640.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 = 10.0 fragment_mass_units = 1 calibrate_mass = 2 use_all_mods_in_first_search = 0 write_calibrated_mzml = 0 write_uncalibrated_mgf = 0 write_mzbin_all = 0 isotope_error = 0/1/2/3 mass_offsets = 0.0 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 = 2 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 = 50.0 report_alternative_proteins = 1 override_charge = 0 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 = 4 minimum_ratio = 0.0 intensity_transform = 1 activation_types = all group_variable = 0 require_precursor = 1 reuse_dia_fragment_peaks = 0 remove_precursor_peak = 0 remove_precursor_range = -1.500000,1.500000 clear_mz_range_low = 0.0 clear_mz_range_high = 0.0 excluded_scan_list_file = mass_diff_to_variable_mod = 0 min_sequence_matches = 2 check_spectral_files = 1 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 addO

fcyu commented 8 months ago

Hi Tim,

The files were truncated by GitHub. It happens when you reply the message by email but not directly in GitHub. Could you go to https://github.com/Nesvilab/FragPipe/issues/1340 and upload your files there?

Thanks,

Fengchao

TimKarr commented 8 months ago

Hi Fengchao, Here are two zipped files discussed earlier by email. Thank you.

#1_log_2023-11-22_08-57-33.zip #2_log_2023-11-21_21-07-52.zip

fcyu commented 8 months ago

Something was wrong when loading one of your raw files. Could you convert your files to the mzML format (https://fragpipe.nesvilab.org/docs/tutorial_convert.html) and try again?

Thanks,

Fengchao

TimKarr commented 8 months ago

Hi Fenchao,

Thanks, will do (although this has also caused the same issue before). Should say that these same files were also successfully processed by Metamorpheus. Still unclear how Fragpipe could process these files but not for LFQ?

Cheers, Tim

-- Timothy L. Karr, PhD ASU-Banner Neurodegenerative Disease Research Center Assistant Director, KE Operations Manager, Biosciences Mass Spec/Proteomics Core Associate Research Professor, Biodesign Institute Associate Editor, Molecular and Cellular Proteomics https://cores.research.asu.edu/mass-spec/about @.***

From: Fengchao @.> Sent: Wednesday, November 22, 2023 10:40 AM To: Nesvilab/FragPipe @.> Cc: Timothy Karr @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] There were issues when load the Thermo raw files. (Issue #1340)

Something was wrong when loading one of your raw files. Could you convert your files to the mzML format (https://fragpipe.nesvilab.org/docs/tutorial_convert.htmlhttps://urldefense.com/v3/__https:/fragpipe.nesvilab.org/docs/tutorial_convert.html__;!!IKRxdwAv5BmarQ!bqF46b2t5cahNipvP_ZAHjXa_E0UQxF4g7AjFo9cLeZQvI6411ABS8zkB6Wj93NaqhmmUVRZiT84eyNr4N4V5w$) and try again?

Thanks,

Fengchao

— Reply to this email directly, view it on GitHubhttps://urldefense.com/v3/__https:/github.com/Nesvilab/FragPipe/issues/1340*issuecomment-1823211878__;Iw!!IKRxdwAv5BmarQ!bqF46b2t5cahNipvP_ZAHjXa_E0UQxF4g7AjFo9cLeZQvI6411ABS8zkB6Wj93NaqhmmUVRZiT84eyOb07CUhw$, or unsubscribehttps://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/APOK4XH4ISKSSLXA6COTUPLYFY2IFAVCNFSM6AAAAAA7R7UVIWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMRTGIYTCOBXHA__;!!IKRxdwAv5BmarQ!bqF46b2t5cahNipvP_ZAHjXa_E0UQxF4g7AjFo9cLeZQvI6411ABS8zkB6Wj93NaqhmmUVRZiT84eyNlig5xrg$. You are receiving this because you authored the thread.Message ID: @.**@.>>

fcyu commented 8 months ago

The errors you got were random, as you can see that there was no error using the default workflow. I think if you run LFQ-MBR workflow to get the error and run the default workflow again, you probably will see the same error. It like due to some process or configurations in your computer. Converting the files to raw will save you all those troubles.

Thanks, will do (although this has also caused the same issue before)

I guess the errors are different. But please send me the log file if you see errors with the mzML files.

Best,

Fengchao