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Nesvilab / FragPipe

A cross-platform proteomics data analysis suite
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File system issue breaks FragPipe. #943

Closed yishai99 closed 1 year ago

yishai99 commented 1 year ago

Hi, I tried processing Thermo raw data (DDA runs) in Frappe 19. The error I get is: java.lang.IllegalArgumentException: No matching mzml/mgf file for QEP2_GVAI_10_12-11-01563_10_1_230316_uncalibrated.pin, please check that provided mzml/mgf directories contain proper mzml/mgf files. at Features.PinMzmlMatcher.(PinMzmlMatcher.java:94) at Features.MainClass.main(MainClass.java:507)

Not sure what can be done. Attached is the log. Thanks,

Yishai [Uploading log_2022-12-20_11-47-42.txt…]()

fcyu commented 1 year ago

Hi Yishai,

The log file was not attached correctly. Could you send it to yufe AT umich.edu?

Thanks,

Fengchao

fcyu commented 1 year ago

Hi Yishai,

Your log file has been well received. It seems to be a bug in MSBooster. Need Kevin to take a look.

Best,

Fengchao log_2022-12-20_11-47-42.txt

anesvi commented 1 year ago

Hi Yishai, I am wondering why are you running from _uncalibrated.mzML and not from the original files?

From: Fengchao @.> Sent: Wednesday, December 21, 2022 9:29 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] Error when processing an LFQ-MBR workflow (Issue #943)

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Hi Yishai,

Your log file has been well received. It seems to be a bug in MSBooster. Need Kevin to take a look.

Best,

Fengchao log_2022-12-20_11-47-42.txthttps://github.com/Nesvilab/FragPipe/files/10278492/log_2022-12-20_11-47-42.txt

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/943#issuecomment-1361383008, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM64MQLJPIRHONT52VLTWOMH37ANCNFSM6AAAAAATEJSLJI. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>

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yishai99 commented 1 year ago

It was part of troubleshooting. I first tried from the raw files. Got the same error.

On 21 Dec 2022, at 17:03, Alexey Nesvizhskii @.***> wrote:

Hi Yishai, I am wondering why are you running from _uncalibrated.mzML and not from the original files?

From: Fengchao @.> Sent: Wednesday, December 21, 2022 9:29 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] Error when processing an LFQ-MBR workflow (Issue #943)

External Email - Use Caution

Hi Yishai,

Your log file has been well received. It seems to be a bug in MSBooster. Need Kevin to take a look.

Best,

Fengchao log_2022-12-20_11-47-42.txthttps://github.com/Nesvilab/FragPipe/files/10278492/log_2022-12-20_11-47-42.txt

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/943#issuecomment-1361383008, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM64MQLJPIRHONT52VLTWOMH37ANCNFSM6AAAAAATEJSLJI. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>

Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues — Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/943#issuecomment-1361448974, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE5PDYZK5S25O7YOEFYE3D3WOML45ANCNFSM6AAAAAATEJSLJI. You are receiving this because you authored the thread.

yangkl96 commented 1 year ago

Hi Yishai,

I was able to reproduce your issue by searching from an uncalibrated.mzml. Could you try renaming your mzml files to not have "_uncalibrated", i.e. QEP2_GVAI_10_12-11-01563_10_1_230316_uncalibrated.mzML to QEP2_GVAI_10_12-11-01563_10_1_230316.mzML? Then redo the search and MSBooster step.

I wasn't able to reproduce the raw file issue. Do you have a log file searching from the raw files that I can look at?

Thanks, Kevin

yishai99 commented 1 year ago

Here’s the log file when using .raw files of the same experiment. 

On 21 Dec 2022, at 19:46, yangkl96 @.***> wrote:

Hi Yishai,

I was able to reproduce your issue by searching from an uncalibrated.mzml. Could you try renaming your mzml files to not have "_uncalibrated", i.e. QEP2_GVAI_10_12-11-01563_10_1_230316_uncalibrated.mzML to QEP2_GVAI_10_12-11-01563_10_1_230316.mzML? Then redo the search and MSBooster step.

I wasn't able to reproduce the raw file issue. Do you have a log file searching from the raw files that I can look at?

Thanks, Kevin

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/FragPipe/issues/943#issuecomment-1361749404, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE5PDY2SRREJPEOKMWSBHGDWOM7AXANCNFSM6AAAAAATEJSLJI. You are receiving this because you authored the thread.

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 19.0 MSFragger version 3.6 IonQuant version 1.8.9 Philosopher version N/A

LCMS files: Experiment/Group: QEP2_GVAI_10_12_11_01563_10_1_230316

124 commands to execute: CheckCentroid C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" com.dmtavt.fragpipe.util.CheckCentroid D:\Vainer\QEP2_GVAI_10_12-11-01563_10_1_230316.raw 30 MSFragger [Work dir: D:\Vainer\MSFragger] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx110G C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\MSFragger-3.6.jar D:\Vainer\MSFragger\fragger.params D:\Vainer\QEP2_GVAI_10_12-11-01563_10_1_230316.raw D:\Vainer\QEP2_GVAI_11_13-05197_5_1_230316.raw D:\Vainer\QEP2_GVAI_12_13-29969_9_1_230316.raw D:\Vainer\QEP2_GVAI_13_13-08345_8_1_230316.raw D:\Vainer\QEP2_GVAI_14_14-19587_1_7_1_230316.raw D:\Vainer\QEP2_GVAI_15_14-28322_1_9_1_230316.raw D:\Vainer\QEP2_GVAI_16_14-30497_1_6_1_230316.raw D:\Vainer\QEP2_GVAI_17_14-00750_2_4_1_230316.raw D:\Vainer\QEP2_GVAI_18_15-17306_1_4_1_230316.raw D:\Vainer\QEP2_GVAI_19_14-30497_1_6_2_1_230316.raw D:\Vainer\QEP2_GVAI_1_08-11-13549_9_1_230316.raw D:\Vainer\QEP2_GVAI_20_14-00750_2_4_2_1_230316.raw D:\Vainer\QEP2_GVAI_2_09-11-17644_8_1_230316.raw D:\Vainer\QEP2_GVAI_3_10-11-02301_4_1_230316.raw D:\Vainer\QEP2_GVAI_4_11-11-18847_8_1_230316.raw D:\Vainer\QEP2_GVAI_5_12-11-15617_10_1_230316.raw D:\Vainer\QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111.raw D:\Vainer\QEP2_GVAI_7_12-11-06592_6_1_230316.raw D:\Vainer\QEP2_GVAI_8_12-11-06288_6_1_230316.raw D:\Vainer\QEP2_GVAI_9_12-11-14297_9_1_230316.raw MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_10_12-11-01563_10_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_10_12_11_01563_10_1_230316\QEP2_GVAI_10_12-11-01563_10_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_10_12-11-01563_10_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_10_12_11_01563_10_1_230316\QEP2_GVAI_10_12-11-01563_10_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_11_13-05197_5_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_11_13_05197_5_1_230316\QEP2_GVAI_11_13-05197_5_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_11_13-05197_5_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_11_13_05197_5_1_230316\QEP2_GVAI_11_13-05197_5_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_12_13-29969_9_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_12_13_29969_9_1_230316\QEP2_GVAI_12_13-29969_9_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_12_13-29969_9_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_12_13_29969_9_1_230316\QEP2_GVAI_12_13-29969_9_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_13_13-08345_8_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_13_13_08345_8_1_230316\QEP2_GVAI_13_13-08345_8_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_13_13-08345_8_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_13_13_08345_8_1_230316\QEP2_GVAI_13_13-08345_8_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_14_14-19587_1_7_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_14_14_19587_1_7_1_230316\QEP2_GVAI_14_14-19587_1_7_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_14_14-19587_1_7_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_14_14_19587_1_7_1_230316\QEP2_GVAI_14_14-19587_1_7_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_15_14-28322_1_9_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_15_14_28322_1_9_1_230316\QEP2_GVAI_15_14-28322_1_9_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_15_14-28322_1_9_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_15_14_28322_1_9_1_230316\QEP2_GVAI_15_14-28322_1_9_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_16_14-30497_1_6_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_16_14_30497_1_6_1_230316\QEP2_GVAI_16_14-30497_1_6_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_16_14-30497_1_6_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_16_14_30497_1_6_1_230316\QEP2_GVAI_16_14-30497_1_6_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_17_14-00750_2_4_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_17_14_00750_2_4_1_230316\QEP2_GVAI_17_14-00750_2_4_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_17_14-00750_2_4_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_17_14_00750_2_4_1_230316\QEP2_GVAI_17_14-00750_2_4_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_18_15-17306_1_4_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_18_15_17306_1_4_1_230316\QEP2_GVAI_18_15-17306_1_4_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_18_15-17306_1_4_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_18_15_17306_1_4_1_230316\QEP2_GVAI_18_15-17306_1_4_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_19_14-30497_1_6_2_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_19_14_30497_1_6_2_1_230316\QEP2_GVAI_19_14-30497_1_6_2_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_19_14-30497_1_6_2_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_19_14_30497_1_6_2_1_230316\QEP2_GVAI_19_14-30497_1_6_2_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_1_08-11-13549_9_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_1_08_11_13549_9_1_230316\QEP2_GVAI_1_08-11-13549_9_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_1_08-11-13549_9_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_1_08_11_13549_9_1_230316\QEP2_GVAI_1_08-11-13549_9_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_20_14-00750_2_4_2_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_20_14_00750_2_4_2_1_230316\QEP2_GVAI_20_14-00750_2_4_2_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_20_14-00750_2_4_2_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_20_14_00750_2_4_2_1_230316\QEP2_GVAI_20_14-00750_2_4_2_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_2_09-11-17644_8_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_2_09_11_17644_8_1_230316\QEP2_GVAI_2_09-11-17644_8_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_2_09-11-17644_8_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_2_09_11_17644_8_1_230316\QEP2_GVAI_2_09-11-17644_8_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_3_10-11-02301_4_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_3_10_11_02301_4_1_230316\QEP2_GVAI_3_10-11-02301_4_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_3_10-11-02301_4_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_3_10_11_02301_4_1_230316\QEP2_GVAI_3_10-11-02301_4_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_4_11-11-18847_8_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_4_11_11_18847_8_1_230316\QEP2_GVAI_4_11-11-18847_8_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_4_11-11-18847_8_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_4_11_11_18847_8_1_230316\QEP2_GVAI_4_11-11-18847_8_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_5_12-11-15617_10_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_5_12_11_15617_10_1_230316\QEP2_GVAI_5_12-11-15617_10_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_5_12-11-15617_10_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_5_12_11_15617_10_1_230316\QEP2_GVAI_5_12-11-15617_10_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111.pepXML D:\Vainer\MSFragger\QEP2_GVAI_6_12_11_12402_4_1_230316_160402173111\QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111.pin D:\Vainer\MSFragger\QEP2_GVAI_6_12_11_12402_4_1_230316_160402173111\QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_7_12-11-06592_6_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_7_12_11_06592_6_1_230316\QEP2_GVAI_7_12-11-06592_6_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_7_12-11-06592_6_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_7_12_11_06592_6_1_230316\QEP2_GVAI_7_12-11-06592_6_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_8_12-11-06288_6_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_8_12_11_06288_6_1_230316\QEP2_GVAI_8_12-11-06288_6_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_8_12-11-06288_6_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_8_12_11_06288_6_1_230316\QEP2_GVAI_8_12-11-06288_6_1_230316.pin MSFragger move pepxml C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_9_12-11-14297_9_1_230316.pepXML D:\Vainer\MSFragger\QEP2_GVAI_9_12_11_14297_9_1_230316\QEP2_GVAI_9_12-11-14297_9_1_230316.pepXML MSFragger move pin C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar;/C:/Users/protolab/Downloads/FragPipe-jre-19.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err D:\Vainer\QEP2_GVAI_9_12-11-14297_9_1_230316.pin D:\Vainer\MSFragger\QEP2_GVAI_9_12_11_14297_9_1_230316\QEP2_GVAI_9_12-11-14297_9_1_230316.pin MSBooster [Work dir: D:\Vainer\MSFragger] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\msbooster-1.1.10.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar" Features.MainClass --paramsList D:\Vainer\MSFragger\msbooster_params.txt Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_12_13_29969_9_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_12_13-29969_9_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_12_13-29969_9_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_12_13-29969_9_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_2_09_11_17644_8_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_2_09-11-17644_8_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_2_09-11-17644_8_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_2_09-11-17644_8_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_15_14_28322_1_9_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_15_14-28322_1_9_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_15_14-28322_1_9_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_15_14-28322_1_9_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_5_12_11_15617_10_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_5_12-11-15617_10_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_5_12-11-15617_10_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_5_12-11-15617_10_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_11_13_05197_5_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_11_13-05197_5_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_11_13-05197_5_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_11_13-05197_5_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_3_10_11_02301_4_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_3_10-11-02301_4_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_3_10-11-02301_4_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_3_10-11-02301_4_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_10_12_11_01563_10_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_10_12-11-01563_10_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_10_12-11-01563_10_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_10_12-11-01563_10_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_16_14_30497_1_6_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_16_14-30497_1_6_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_16_14-30497_1_6_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_16_14-30497_1_6_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_18_15_17306_1_4_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_18_15-17306_1_4_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_18_15-17306_1_4_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_18_15-17306_1_4_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_14_14_19587_1_7_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_14_14-19587_1_7_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_14_14-19587_1_7_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_14_14-19587_1_7_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_17_14_00750_2_4_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_17_14-00750_2_4_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_17_14-00750_2_4_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_17_14-00750_2_4_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_20_14_00750_2_4_2_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_20_14-00750_2_4_2_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_20_14-00750_2_4_2_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_20_14-00750_2_4_2_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_6_12_11_12402_4_1_230316_160402173111] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111_percolator_decoy_psms.tsv QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_1_08_11_13549_9_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_1_08-11-13549_9_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_1_08-11-13549_9_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_1_08-11-13549_9_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_9_12_11_14297_9_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_9_12-11-14297_9_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_9_12-11-14297_9_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_9_12-11-14297_9_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_8_12_11_06288_6_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_8_12-11-06288_6_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_8_12-11-06288_6_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_8_12-11-06288_6_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_19_14_30497_1_6_2_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_19_14-30497_1_6_2_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_19_14-30497_1_6_2_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_19_14-30497_1_6_2_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_4_11_11_18847_8_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_4_11-11-18847_8_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_4_11-11-18847_8_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_4_11-11-18847_8_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_13_13_08345_8_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_13_13-08345_8_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_13_13-08345_8_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_13_13-08345_8_1_230316_edited.pin Percolator [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_7_12_11_06592_6_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\percolator-305\percolator.exe --only-psms --no-terminate --post-processing-tdc --num-threads 30 --results-psms QEP2_GVAI_7_12-11-06592_6_1_230316_percolator_target_psms.tsv --decoy-results-psms QEP2_GVAI_7_12-11-06592_6_1_230316_percolator_decoy_psms.tsv QEP2_GVAI_7_12-11-06592_6_1_230316_edited.pin Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_12_13_29969_9_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_12_13-29969_9_1_230316.pin QEP2_GVAI_12_13-29969_9_1_230316 QEP2_GVAI_12_13-29969_9_1_230316_percolator_target_psms.tsv QEP2_GVAI_12_13-29969_9_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_12_13-29969_9_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_12_13_29969_9_1_230316\QEP2_GVAI_12_13-29969_9_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_12_13_29969_9_1_230316\QEP2_GVAI_12_13-29969_9_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_2_09_11_17644_8_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_2_09-11-17644_8_1_230316.pin QEP2_GVAI_2_09-11-17644_8_1_230316 QEP2_GVAI_2_09-11-17644_8_1_230316_percolator_target_psms.tsv QEP2_GVAI_2_09-11-17644_8_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_2_09-11-17644_8_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_2_09_11_17644_8_1_230316\QEP2_GVAI_2_09-11-17644_8_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_2_09_11_17644_8_1_230316\QEP2_GVAI_2_09-11-17644_8_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_15_14_28322_1_9_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_15_14-28322_1_9_1_230316.pin QEP2_GVAI_15_14-28322_1_9_1_230316 QEP2_GVAI_15_14-28322_1_9_1_230316_percolator_target_psms.tsv QEP2_GVAI_15_14-28322_1_9_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_15_14-28322_1_9_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_15_14_28322_1_9_1_230316\QEP2_GVAI_15_14-28322_1_9_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_15_14_28322_1_9_1_230316\QEP2_GVAI_15_14-28322_1_9_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_5_12_11_15617_10_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_5_12-11-15617_10_1_230316.pin QEP2_GVAI_5_12-11-15617_10_1_230316 QEP2_GVAI_5_12-11-15617_10_1_230316_percolator_target_psms.tsv QEP2_GVAI_5_12-11-15617_10_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_5_12-11-15617_10_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_5_12_11_15617_10_1_230316\QEP2_GVAI_5_12-11-15617_10_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_5_12_11_15617_10_1_230316\QEP2_GVAI_5_12-11-15617_10_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_11_13_05197_5_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_11_13-05197_5_1_230316.pin QEP2_GVAI_11_13-05197_5_1_230316 QEP2_GVAI_11_13-05197_5_1_230316_percolator_target_psms.tsv QEP2_GVAI_11_13-05197_5_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_11_13-05197_5_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_11_13_05197_5_1_230316\QEP2_GVAI_11_13-05197_5_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_11_13_05197_5_1_230316\QEP2_GVAI_11_13-05197_5_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_3_10_11_02301_4_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_3_10-11-02301_4_1_230316.pin QEP2_GVAI_3_10-11-02301_4_1_230316 QEP2_GVAI_3_10-11-02301_4_1_230316_percolator_target_psms.tsv QEP2_GVAI_3_10-11-02301_4_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_3_10-11-02301_4_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_3_10_11_02301_4_1_230316\QEP2_GVAI_3_10-11-02301_4_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_3_10_11_02301_4_1_230316\QEP2_GVAI_3_10-11-02301_4_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_10_12_11_01563_10_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_10_12-11-01563_10_1_230316.pin QEP2_GVAI_10_12-11-01563_10_1_230316 QEP2_GVAI_10_12-11-01563_10_1_230316_percolator_target_psms.tsv QEP2_GVAI_10_12-11-01563_10_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_10_12-11-01563_10_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_10_12_11_01563_10_1_230316\QEP2_GVAI_10_12-11-01563_10_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_10_12_11_01563_10_1_230316\QEP2_GVAI_10_12-11-01563_10_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_16_14_30497_1_6_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_16_14-30497_1_6_1_230316.pin QEP2_GVAI_16_14-30497_1_6_1_230316 QEP2_GVAI_16_14-30497_1_6_1_230316_percolator_target_psms.tsv QEP2_GVAI_16_14-30497_1_6_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_16_14-30497_1_6_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_16_14_30497_1_6_1_230316\QEP2_GVAI_16_14-30497_1_6_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_16_14_30497_1_6_1_230316\QEP2_GVAI_16_14-30497_1_6_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_18_15_17306_1_4_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_18_15-17306_1_4_1_230316.pin QEP2_GVAI_18_15-17306_1_4_1_230316 QEP2_GVAI_18_15-17306_1_4_1_230316_percolator_target_psms.tsv QEP2_GVAI_18_15-17306_1_4_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_18_15-17306_1_4_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_18_15_17306_1_4_1_230316\QEP2_GVAI_18_15-17306_1_4_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_18_15_17306_1_4_1_230316\QEP2_GVAI_18_15-17306_1_4_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_14_14_19587_1_7_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_14_14-19587_1_7_1_230316.pin QEP2_GVAI_14_14-19587_1_7_1_230316 QEP2_GVAI_14_14-19587_1_7_1_230316_percolator_target_psms.tsv QEP2_GVAI_14_14-19587_1_7_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_14_14-19587_1_7_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_14_14_19587_1_7_1_230316\QEP2_GVAI_14_14-19587_1_7_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_14_14_19587_1_7_1_230316\QEP2_GVAI_14_14-19587_1_7_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_17_14_00750_2_4_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_17_14-00750_2_4_1_230316.pin QEP2_GVAI_17_14-00750_2_4_1_230316 QEP2_GVAI_17_14-00750_2_4_1_230316_percolator_target_psms.tsv QEP2_GVAI_17_14-00750_2_4_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_17_14-00750_2_4_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_17_14_00750_2_4_1_230316\QEP2_GVAI_17_14-00750_2_4_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_17_14_00750_2_4_1_230316\QEP2_GVAI_17_14-00750_2_4_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_20_14_00750_2_4_2_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_20_14-00750_2_4_2_1_230316.pin QEP2_GVAI_20_14-00750_2_4_2_1_230316 QEP2_GVAI_20_14-00750_2_4_2_1_230316_percolator_target_psms.tsv QEP2_GVAI_20_14-00750_2_4_2_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_20_14-00750_2_4_2_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_20_14_00750_2_4_2_1_230316\QEP2_GVAI_20_14-00750_2_4_2_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_20_14_00750_2_4_2_1_230316\QEP2_GVAI_20_14-00750_2_4_2_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_6_12_11_12402_4_1_230316_160402173111] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111.pin QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111 QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111_percolator_target_psms.tsv QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111_percolator_decoy_psms.tsv interact-QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_6_12_11_12402_4_1_230316_160402173111\QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_6_12_11_12402_4_1_230316_160402173111\QEP2_GVAI_6_12-11-12402_4_1_230316_160402173111_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_1_08_11_13549_9_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_1_08-11-13549_9_1_230316.pin QEP2_GVAI_1_08-11-13549_9_1_230316 QEP2_GVAI_1_08-11-13549_9_1_230316_percolator_target_psms.tsv QEP2_GVAI_1_08-11-13549_9_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_1_08-11-13549_9_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_1_08_11_13549_9_1_230316\QEP2_GVAI_1_08-11-13549_9_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_1_08_11_13549_9_1_230316\QEP2_GVAI_1_08-11-13549_9_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_9_12_11_14297_9_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_9_12-11-14297_9_1_230316.pin QEP2_GVAI_9_12-11-14297_9_1_230316 QEP2_GVAI_9_12-11-14297_9_1_230316_percolator_target_psms.tsv QEP2_GVAI_9_12-11-14297_9_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_9_12-11-14297_9_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_9_12_11_14297_9_1_230316\QEP2_GVAI_9_12-11-14297_9_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_9_12_11_14297_9_1_230316\QEP2_GVAI_9_12-11-14297_9_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_8_12_11_06288_6_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_8_12-11-06288_6_1_230316.pin QEP2_GVAI_8_12-11-06288_6_1_230316 QEP2_GVAI_8_12-11-06288_6_1_230316_percolator_target_psms.tsv QEP2_GVAI_8_12-11-06288_6_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_8_12-11-06288_6_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_8_12_11_06288_6_1_230316\QEP2_GVAI_8_12-11-06288_6_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_8_12_11_06288_6_1_230316\QEP2_GVAI_8_12-11-06288_6_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_19_14_30497_1_6_2_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_19_14-30497_1_6_2_1_230316.pin QEP2_GVAI_19_14-30497_1_6_2_1_230316 QEP2_GVAI_19_14-30497_1_6_2_1_230316_percolator_target_psms.tsv QEP2_GVAI_19_14-30497_1_6_2_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_19_14-30497_1_6_2_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_19_14_30497_1_6_2_1_230316\QEP2_GVAI_19_14-30497_1_6_2_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_19_14_30497_1_6_2_1_230316\QEP2_GVAI_19_14-30497_1_6_2_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_4_11_11_18847_8_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_4_11-11-18847_8_1_230316.pin QEP2_GVAI_4_11-11-18847_8_1_230316 QEP2_GVAI_4_11-11-18847_8_1_230316_percolator_target_psms.tsv QEP2_GVAI_4_11-11-18847_8_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_4_11-11-18847_8_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_4_11_11_18847_8_1_230316\QEP2_GVAI_4_11-11-18847_8_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_4_11_11_18847_8_1_230316\QEP2_GVAI_4_11-11-18847_8_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_13_13_08345_8_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_13_13-08345_8_1_230316.pin QEP2_GVAI_13_13-08345_8_1_230316 QEP2_GVAI_13_13-08345_8_1_230316_percolator_target_psms.tsv QEP2_GVAI_13_13-08345_8_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_13_13-08345_8_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_13_13_08345_8_1_230316\QEP2_GVAI_13_13-08345_8_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_13_13_08345_8_1_230316\QEP2_GVAI_13_13-08345_8_1_230316_percolator_decoy_psms.tsv Percolator: Convert to pepxml [Work dir: D:\Vainer\MSFragger\QEP2_GVAI_7_12_11_06592_6_1_230316] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib/ com.dmtavt.fragpipe.tools.percolator.PercolatorOutputToPepXML QEP2_GVAI_7_12-11-06592_6_1_230316.pin QEP2_GVAI_7_12-11-06592_6_1_230316 QEP2_GVAI_7_12-11-06592_6_1_230316_percolator_target_psms.tsv QEP2_GVAI_7_12-11-06592_6_1_230316_percolator_decoy_psms.tsv interact-QEP2_GVAI_7_12-11-06592_6_1_230316 DDA 0.5 Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_7_12_11_06592_6_1_230316\QEP2_GVAI_7_12-11-06592_6_1_230316_percolator_target_psms.tsv Percolator: Delete temp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -cp C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\lib\fragpipe-19.0.jar com.github.chhh.utils.FileDelete D:\Vainer\MSFragger\QEP2_GVAI_7_12_11_06592_6_1_230316\QEP2_GVAI_7_12-11-06592_6_1_230316_percolator_decoy_psms.tsv IonQuant [Work dir: D:\Vainer\MSFragger] C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\jre\bin\java.exe -Xmx110G -Dlibs.bruker.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\bruker" -Dlibs.thermo.dir="C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.6\ext\thermo" -cp "C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\jfreechart-1.5.3.jar;C:\Users\protolab\Downloads\FragPipe-jre-19.0\fragpipe\tools\batmass-io-1.28.8.jar;C:\Users\protolab\Downloads\FragPipe-jre-18.0\fragpipe\tools\IonQuant-1.8.9.jar" ionquant.IonQuant --threads 30 --ionmobility 0 --minexps 1 --mbr 1 --maxlfq 1 --requantify 1 --mztol 10 --imtol 0.05 --rttol 0.4 --mbrmincorr 0 --mbrrttol 1 --mbrimtol 0.05 --mbrtoprun 10 --ionfdr 0.01 --proteinfdr 1 --peptidefdr 1 --normalization 1 --minisotopes 2 --minscans 3 --writeindex 0 --tp 0 --minfreq 0 --minions 2 --locprob 0.75 --uniqueness 0 --multidir . --filelist D:\Vainer\MSFragger\filelist_ionquant.txt --modlist D:\Vainer\MSFragger\modmasses_ionquant.txt


Execution order:

    Cmd: [START], Work dir: [D:\Vainer\MSFragger]
    Cmd: [CheckCentroid], Work dir: [D:\Vainer\MSFragger]
    Cmd: [MSFragger], Work dir: [D:\Vainer\MSFragger]
    Cmd: [MSBooster], Work dir: [D:\Vainer\MSFragger]
    Cmd: [Percolator], Work dir: [D:\Vainer\MSFragger]
    Cmd: [IonQuant], Work dir: [D:\Vainer\MSFragger]

>contam_sp|O00762|UBE2C_HUMAN Ubiquitin-conjugating enzyme E2 C OS=Homo sapiens GN=UBE2C PE=1 SV=1
>rev_sp|O43237|DC1L2_HUMAN Cytoplasmic dynein 1 light intermediate chain 2 OS=Homo sapiens OX=9606 GN=DYNC1LI2 PE=1 SV=1
>rev_sp|P0CJ87|DU4L4_HUMAN Double homeobox protein 4-like protein 4 OS=Homo sapiens OX=9606 GN=DUX4L4 PE=3 SV=1
>rev_sp|P49356|FNTB_HUMAN Protein farnesyltransferase subunit beta OS=Homo sapiens OX=9606 GN=FNTB PE=1 SV=1
>rev_sp|Q14093|CYLC2_HUMAN Cylicin-2 OS=Homo sapiens OX=9606 GN=CYLC2 PE=2 SV=1
>rev_sp|Q68CP4|HGNAT_HUMAN Heparan-alpha-glucosaminide N-acetyltransferase OS=Homo sapiens OX=9606 GN=HGSNAT PE=1 SV=2

>rev_sp|Q8IVQ6|ZDH21_HUMAN Palmitoyltransferase ZDHHC21 OS=Homo sapiens OX=9606 GN=ZDHHC21 PE=1 SV=1
>rev_sp|Q8WUN7|UBTD2_HUMAN Ubiquitin domain-containing protein 2 OS=Homo sapiens OX=9606 GN=UBTD2 PE=1 SV=2
>rev_sp|Q9BQA9|CYBC1_HUMAN Cytochrome b-245 chaperone 1 OS=Homo sapiens OX=9606 GN=CYBC1 PE=1 SV=1
>rev_sp|Q9NST1|PLPL3_HUMAN 1-acylglycerol-3-phosphate O-acyltransferase PNPLA3 OS=Homo sapiens OX=9606 GN=PNPLA3 PE=1 SV=2
>rev_sp|Q9Y673|ALG5_HUMAN Dolichyl-phosphate beta-glucosyltransferase OS=Homo sapiens OX=9606 GN=ALG5 PE=1 SV=1
>sp|O43572|AKA10_HUMAN A-kinase anchor protein 10, mitochondrial OS=Homo sapiens OX=9606 GN=AKAP10 PE=1 SV=2
>sp|P0DP06|HVD34_HUMAN Immunoglobulin heavy variable 4-30-4 OS=Homo sapiens OX=9606 GN=IGHV4-30-4 PE=3 SV=1
>sp|P50238|CRIP1_HUMAN Cysteine-rich protein 1 OS=Homo sapiens OX=9606 GN=CRIP1 PE=1 SV=3
>sp|Q14500|KCJ12_HUMAN ATP-sensitive inward rectifier potassium channel 12 OS=Homo sapiens OX=9606 GN=KCNJ12 PE=1 SV=2
>sp|Q6EIG7|CLC6A_HUMAN C-type lectin domain family 6 member A OS=Homo sapiens OX=9606 GN=CLEC6A PE=1 SV=1
>sp|Q8IXB1|DJC10_HUMAN DnaJ homolog subfamily C member 10 OS=Homo sapiens OX=9606 GN=DNAJC10 PE=1 SV=2
>sp|Q8WWH4|ASZ1_HUMAN Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 OS=Homo sapiens OX=9606 GN=ASZ1 PE=1 SV=1
>sp|Q9BRX9|WDR83_HUMAN WD repeat domain-containing protein 83 OS=Homo sapiens OX=9606 GN=WDR83 PE=1 SV=1
>sp|Q9NVE7|PANK4_HUMAN 4'-phosphopantetheine phosphatase OS=Homo sapiens OX=9606 GN=PANK4 PE=1 SV=1
>sp|Q9Y6X6|MYO16_HUMAN Unconventional myosin-XVI OS=Homo sapiens OX=9606 GN=MYO16 PE=1 SV=3

# FragPipe v19.0ui state cache

# Please edit the following path to point to the correct location.
# In Windows, please replace single '\' with '\\'
database.db-path=H\:\\Proteomics\\Databases\\2022_Working_general_DBs\\Human\\2022-01-23-decoys-contam-Human_SP_Jan2022.fasta.fas

Table.editor=79.96633
crystalc.run-crystalc=false
database.decoy-tag=rev_
diann.fragpipe.cmd-opts=
diann.library=
diann.q-value=0.01
diann.quantification-strategy=3
diann.run-dia-nn=false
diann.run-specific-protein-q-value=false
diann.unrelated-runs=false
diann.use-predicted-spectra=true
diaumpire.AdjustFragIntensity=true
diaumpire.BoostComplementaryIon=false
diaumpire.CorrThreshold=0
diaumpire.DeltaApex=0.2
diaumpire.ExportPrecursorPeak=false
diaumpire.Q1=true
diaumpire.Q2=true
diaumpire.Q3=true
diaumpire.RFmax=500
diaumpire.RPmax=25
diaumpire.RTOverlap=0.3
diaumpire.SE.EstimateBG=false
diaumpire.SE.IsoPattern=0.3
diaumpire.SE.MS1PPM=10
diaumpire.SE.MS2PPM=20
diaumpire.SE.MS2SN=1.1
diaumpire.SE.MassDefectFilter=true
diaumpire.SE.MassDefectOffset=0.1
diaumpire.SE.NoMissedScan=1
diaumpire.SE.SN=1.1
diaumpire.run-diaumpire=false
fragpipe-config.bin-ionquant=C\:\\Users\\protolab\\Downloads\\FragPipe-jre-18.0\\fragpipe\\tools\\IonQuant-1.8.9.jar
fragpipe-config.bin-msfragger=C\:\\Users\\protolab\\Downloads\\FragPipe-jre-18.0\\fragpipe\\tools\\MSFragger-3.6\\MSFragger-3.6.jar
fragpipe-config.bin-philosopher=C\:\\Users\\protolab\\Downloads\\FragPipe-jre-18.0\\fragpipe\\tools\\philosopher_v4.2.2_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.minexps=1
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.proteinquant=2
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.data_type=0
msfragger.deisotope=1
msfragger.delta_mass_exclude_ranges=(-1.5,3.5)
msfragger.deneutralloss=1
msfragger.diagnostic_fragments=
msfragger.diagnostic_intensity_filter=0
msfragger.digest_max_length=50
msfragger.digest_min_length=7
msfragger.fragment_ion_series=b,y
msfragger.fragment_mass_tolerance=20
msfragger.fragment_mass_units=1
msfragger.intensity_transform=0
msfragger.ion_series_definitions=
msfragger.isotope_error=0/1/2
msfragger.labile_search_mode=off
msfragger.localize_delta_mass=false
msfragger.mass_diff_to_variable_mod=0
msfragger.mass_offsets=0
msfragger.max_fragment_charge=2
msfragger.max_variable_mods_combinations=5000
msfragger.max_variable_mods_per_peptide=3
msfragger.min_fragments_modelling=2
msfragger.min_matched_fragments=4
msfragger.min_sequence_matches=2
msfragger.minimum_peaks=15
msfragger.minimum_ratio=0.01
msfragger.misc.fragger.clear-mz-hi=0
msfragger.misc.fragger.clear-mz-lo=0
msfragger.misc.fragger.digest-mass-hi=5000
msfragger.misc.fragger.digest-mass-lo=500
msfragger.misc.fragger.enzyme-dropdown-1=stricttrypsin
msfragger.misc.fragger.enzyme-dropdown-2=null
msfragger.misc.fragger.precursor-charge-hi=4
msfragger.misc.fragger.precursor-charge-lo=1
msfragger.misc.fragger.remove-precursor-range-hi=1.5
msfragger.misc.fragger.remove-precursor-range-lo=-1.5
msfragger.misc.slice-db=1
msfragger.num_enzyme_termini=2
msfragger.output_format=pepXML_pin
msfragger.output_max_expect=50
msfragger.output_report_topN=1
msfragger.override_charge=false
msfragger.precursor_mass_lower=-20
msfragger.precursor_mass_mode=selected
msfragger.precursor_mass_units=1
msfragger.precursor_mass_upper=20
msfragger.precursor_true_tolerance=20
msfragger.precursor_true_units=1
msfragger.remainder_fragment_masses=
msfragger.remove_precursor_peak=1
msfragger.report_alternative_proteins=true
msfragger.restrict_deltamass_to=all
msfragger.run-msfragger=true
msfragger.search_enzyme_cut_1=KR
msfragger.search_enzyme_cut_2=
msfragger.search_enzyme_name=stricttrypsin
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 (argin
yangkl96 commented 1 year ago

Hi Yishai,

Could you attach the entire log.txt file here, or send to yangkl AT umich.edu? Pasting the contents here cuts off, so I cannot see where the error occurs.

Also, did renaming the mzml files to not have "uncalibrated" resolve the issue?

Thanks, Kevin

yangkl96 commented 1 year ago

log_2022-12-26_12-36-37.txt

Attaching most recent error log

fcyu commented 1 year ago

The error with the raw files was due to a different issue. It looks like the fasta file was deleted in the middle of the job:

java.io.FileNotFoundException: H:\Proteomics\Databases\2022_Working_general_DBs\Human\2022-01-23-decoys-contam-Human_SP_Jan2022.fasta.fas (The system cannot find the path specified)

I guess the fasta file was in a network drive (H:\....).

@yishai99 can you check the file system, and make sure that the files are available and not used by other tools during running FragPipe?

Thanks,

Fengchao

yishai99 commented 1 year ago

Yes, the issue was due to disconnects with the network. Thanks!