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Published 20 hours ago • verified publisher icon Nesvilab

Java or RAM issue?

Open jmcalist opened this issue 1 year ago • 6 comments

  • Describe the issue or question: Hello,

We are trying to run a sizeable data set (64 .raw files, 143GB), I am trying it on Amazon Cloud at 64Gb RAM. I attached the log file, at the end there seems to be java errors, although there are likely others as well. I also attached images of the java version and the system info. If it just needs more RAM I can run on more RAM through AWS, but was hoping 64Gb would be enough :)

Thank you so much for any advice you can provide

All the best,

Jason log_2022-08-26_20-25-36.txt system info java version

  • Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

jmcalist avatar Aug 26 '22 20:08 jmcalist

It is not about the memory.

There are several errors due to different reasons.

  1. Some of your files are corrupted:
Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-36.raw. Will ignore it.
UNAVAILABLE: OS Error
C:\Users\Administrator\Downloads\S22034-Nick-36.raw: Scans = 0
Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-52.raw. Will ignore it.
UNKNOWN
Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-60.raw. Will ignore it.
UNKNOWN
C:\Users\Administrator\Downloads\S22034-Nick-52.raw: Scans = 0
C:\Users\Administrator\Downloads\S22034-Nick-60.raw: Scans = 0
Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-44.raw. Will ignore it.
UNAVAILABLE: io exception
C:\Users\Administrator\Downloads\S22034-Nick-44.raw: Scans = 0
Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-28-2nd.raw. Will ignore it.
UNKNOWN
Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-53.raw. Will ignore it.
UNKNOWN
Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-11.raw. Will ignore it.
UNKNOWN
C:\Users\Administrator\Downloads\S22034-Nick-28-2nd.raw: Scans = 0
C:\Users\Administrator\Downloads\S22034-Nick-53.raw: Scans = 0
C:\Users\Administrator\Downloads\S22034-Nick-11.raw: Scans = 0
  1. There are errors that I never saw. Please double check your files and system.
java.util.concurrent.ExecutionException: java.lang.IndexOutOfBoundsException: Index 63 out of bounds for length 58
	at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
	at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
	at edu.umich.andykong.msfragger.MSFragger.a(Unknown Source)
	at edu.umich.andykong.msfragger.MSFragger.b(Unknown Source)
	at edu.umich.andykong.msfragger.MSFragger.main(Unknown Source)
Caused by: java.lang.IndexOutOfBoundsException: Index 63 out of bounds for length 58
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:100)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:106)
	at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:302)
	at java.base/java.util.Objects.checkIndex(Objects.java:359)
	at java.base/java.util.ArrayList.get(ArrayList.java:427)
	at edu.umich.andykong.msfragger.MSFragger.a(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
	at java.base/java.lang.Thread.run(Thread.java:833)

Best,

Fengchao

fcyu avatar Aug 27 '22 00:08 fcyu

Thanks so much, I tried with the jre version of Fragpipe with Java and it seems to have done better, but looks like it got stuck on sample 49 (logfile attached)

I checked the file for this sample and when I checked the TIC in SeeMS from ProteoWizard, the following error resulted:, do you happen to know what could cause this error?

Thanks so much!

[cid:f72d8a98-8cf9-4d5b-8626-d07dfa0b1d21]

From: Fengchao @.> Sent: Friday, August 26, 2022 8:45 PM To: Nesvilab/FragPipe @.> Cc: Jason Mcalister @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Java or RAM issue? (Issue #809)

CAUTION: This email originated from outside of the University of Guelph. Do not click links or open attachments unless you recognize the sender and know the content is safe. If in doubt, forward suspicious emails to @.***

It is not about the memory.

There are several errors due to different reasons.

  1. Some of your files are corrupted:

Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-36.raw. Will ignore it. UNAVAILABLE: OS Error C:\Users\Administrator\Downloads\S22034-Nick-36.raw: Scans = 0 Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-52.raw. Will ignore it. UNKNOWN Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-60.raw. Will ignore it. UNKNOWN C:\Users\Administrator\Downloads\S22034-Nick-52.raw: Scans = 0 C:\Users\Administrator\Downloads\S22034-Nick-60.raw: Scans = 0 Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-44.raw. Will ignore it. UNAVAILABLE: io exception C:\Users\Administrator\Downloads\S22034-Nick-44.raw: Scans = 0 Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-28-2nd.raw. Will ignore it. UNKNOWN Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-53.raw. Will ignore it. UNKNOWN Failed in checking C:\Users\Administrator\Downloads\S22034-Nick-11.raw. Will ignore it. UNKNOWN C:\Users\Administrator\Downloads\S22034-Nick-28-2nd.raw: Scans = 0 C:\Users\Administrator\Downloads\S22034-Nick-53.raw: Scans = 0 C:\Users\Administrator\Downloads\S22034-Nick-11.raw: Scans = 0

  1. There are errors that I never saw. Please double check your files and system.

java.util.concurrent.ExecutionException: java.lang.IndexOutOfBoundsException: Index 63 out of bounds for length 58 at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191) at edu.umich.andykong.msfragger.MSFragger.a(Unknown Source) at edu.umich.andykong.msfragger.MSFragger.b(Unknown Source) at edu.umich.andykong.msfragger.MSFragger.main(Unknown Source) Caused by: java.lang.IndexOutOfBoundsException: Index 63 out of bounds for length 58 at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:100) at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckIndex(Preconditions.java:106) at java.base/jdk.internal.util.Preconditions.checkIndex(Preconditions.java:302) at java.base/java.util.Objects.checkIndex(Objects.java:359) at java.base/java.util.ArrayList.get(ArrayList.java:427) at edu.umich.andykong.msfragger.MSFragger.a(Unknown Source) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at java.base/java.lang.Thread.run(Thread.java:833)

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/809#issuecomment-1229072683, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARFTQLL6LSGGMPPAPRESUVLV3FQK7ANCNFSM57X62NPQ. You are receiving this because you authored the thread.Message ID: @.***>

System OS: Windows Server 2019, Architecture: AMD64 Java Info: 11.0.9.1, OpenJDK 64-Bit Server VM, AdoptOpenJDK

Version info: FragPipe version 18.0 MSFragger version 3.5 Philosopher version 4.4.0

LCMS files: Experiment/Group: 999

  • C:\Users\Administrator\Downloads\S22034-Nick-1.raw DDA
  • C:\Users\Administrator\Downloads\S22034-Nick-10.raw DDA
  • C:\Users\Administrator\Downloads\S22034-Nick-11.raw DDA
  • C:\Users\Administrator\Downloads\S22034-Nick-12.raw DDA
  • C:\Users\Administrator\Downloads\S22034-Nick-13.raw DDA
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  • C:\Users\Administrator\Downloads\S22034-Nick-2.raw DDA
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  • C:\Users\Administrator\Downloads\S22034-Nick-60.raw DDA
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  • C:\Users\Administrator\Downloads\S22034-Nick-7.raw DDA
  • C:\Users\Administrator\Downloads\S22034-Nick-8.raw DDA
  • C:\Users\Administrator\Downloads\S22034-Nick-9.raw DDA

399 commands to execute: CheckCentroid C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -Xmx57G -cp "C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\tools\batmass-io-1.25.5.jar" com.dmtavt.fragpipe.util.CheckCentroid C:\Users\Administrator\Downloads\S22034-Nick-1.raw 7 WorkspaceCleanInit [Work dir: C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999] C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999] C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ADMINI~1\AppData\Local\Temp\2\e7d2ca7b-878e-4b0e-bfb3-bc437f0a7ad5 WorkspaceCleanInit [Work dir: C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve] C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --clean --nocheck WorkspaceCleanInit [Work dir: C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve] C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\tools\philosopher_v4.4.0_windows_amd64\philosopher.exe workspace --init --nocheck --temp C:\Users\ADMINI~1\AppData\Local\Temp\2\39dd8d6e-7d22-401e-8b1b-1b7d1557d00e MSFragger [Work dir: C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve] C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx57G C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\tools\MSFragger-3.5\MSFragger-3.5.jar C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\fragger.params C:\Users\Administrator\Downloads\S22034-Nick-1.raw C:\Users\Administrator\Downloads\S22034-Nick-10.raw C:\Users\Administrator\Downloads\S22034-Nick-11.raw C:\Users\Administrator\Downloads\S22034-Nick-12.raw C:\Users\Administrator\Downloads\S22034-Nick-13.raw C:\Users\Administrator\Downloads\S22034-Nick-14.raw C:\Users\Administrator\Downloads\S22034-Nick-15.raw C:\Users\Administrator\Downloads\S22034-Nick-16.raw C:\Users\Administrator\Downloads\S22034-Nick-17.raw C:\Users\Administrator\Downloads\S22034-Nick-18.raw C:\Users\Administrator\Downloads\S22034-Nick-19.raw C:\Users\Administrator\Downloads\S22034-Nick-2.raw C:\Users\Administrator\Downloads\S22034-Nick-20.raw C:\Users\Administrator\Downloads\S22034-Nick-21.raw C:\Users\Administrator\Downloads\S22034-Nick-22.raw C:\Users\Administrator\Downloads\S22034-Nick-23.raw C:\Users\Administrator\Downloads\S22034-Nick-24.raw C:\Users\Administrator\Downloads\S22034-Nick-25.raw C:\Users\Administrator\Downloads\S22034-Nick-26.raw C:\Users\Administrator\Downloads\S22034-Nick-27.raw C:\Users\Administrator\Downloads\S22034-Nick-28-2nd.raw C:\Users\Administrator\Downloads\S22034-Nick-29.raw C:\Users\Administrator\Downloads\S22034-Nick-3.raw C:\Users\Administrator\Downloads\S22034-Nick-30.raw C:\Users\Administrator\Downloads\S22034-Nick-31.raw C:\Users\Administrator\Downloads\S22034-Nick-32.raw C:\Users\Administrator\Downloads\S22034-Nick-33.raw C:\Users\Administrator\Downloads\S22034-Nick-34.raw C:\Users\Administrator\Downloads\S22034-Nick-35.raw C:\Users\Administrator\Downloads\S22034-Nick-36.raw C:\Users\Administrator\Downloads\S22034-Nick-37-2nd.raw C:\Users\Administrator\Downloads\S22034-Nick-38.raw C:\Users\Administrator\Downloads\S22034-Nick-39.raw C:\Users\Administrator\Downloads\S22034-Nick-4.raw C:\Users\Administrator\Downloads\S22034-Nick-40.raw C:\Users\Administrator\Downloads\S22034-Nick-41.raw C:\Users\Administrator\Downloads\S22034-Nick-42.raw C:\Users\Administrator\Downloads\S22034-Nick-43.raw C:\Users\Administrator\Downloads\S22034-Nick-44.raw C:\Users\Administrator\Downloads\S22034-Nick-45.raw C:\Users\Administrator\Downloads\S22034-Nick-46.raw C:\Users\Administrator\Downloads\S22034-Nick-47.raw C:\Users\Administrator\Downloads\S22034-Nick-48.raw C:\Users\Administrator\Downloads\S22034-Nick-49.raw C:\Users\Administrator\Downloads\S22034-Nick-5.raw C:\Users\Administrator\Downloads\S22034-Nick-50.raw C:\Users\Administrator\Downloads\S22034-Nick-51.raw C:\Users\Administrator\Downloads\S22034-Nick-52.raw C:\Users\Administrator\Downloads\S22034-Nick-53.raw C:\Users\Administrator\Downloads\S22034-Nick-54.raw C:\Users\Administrator\Downloads\S22034-Nick-55.raw C:\Users\Administrator\Downloads\S22034-Nick-56.raw C:\Users\Administrator\Downloads\S22034-Nick-57.raw C:\Users\Administrator\Downloads\S22034-Nick-58.raw C:\Users\Administrator\Downloads\S22034-Nick-59.raw C:\Users\Administrator\Downloads\S22034-Nick-6.raw C:\Users\Administrator\Downloads\S22034-Nick-60.raw C:\Users\Administrator\Downloads\S22034-Nick-61.raw C:\Users\Administrator\Downloads\S22034-Nick-62.raw C:\Users\Administrator\Downloads\S22034-Nick-63.raw C:\Users\Administrator\Downloads\S22034-Nick-64.raw C:\Users\Administrator\Downloads\S22034-Nick-7.raw C:\Users\Administrator\Downloads\S22034-Nick-8.raw C:\Users\Administrator\Downloads\S22034-Nick-9.raw MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-1.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-1.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-1.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-1.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-10.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-10.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-10.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-10.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-11.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-11.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-11.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-11.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-12.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-12.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-12.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-12.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-13.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-13.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-13.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-13.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-14.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-14.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-14.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-14.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-15.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-15.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-15.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-15.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-16.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-16.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-16.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-16.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-17.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-17.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-17.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-17.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-18.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-18.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-18.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-18.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-19.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-19.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-19.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-19.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-2.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-2.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-2.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-2.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-20.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-20.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-20.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-20.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-21.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-21.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-21.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-21.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-22.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-22.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-22.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-22.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-23.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-23.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-23.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-23.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-24.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-24.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-24.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-24.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-25.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-25.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-25.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-25.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-26.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-26.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-26.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-26.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-27.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-27.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-27.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-27.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-28-2nd.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-28-2nd.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-28-2nd.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-28-2nd.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-29.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-29.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-29.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-29.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-3.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-3.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-3.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-3.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-30.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-30.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp 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C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-31.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-31.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-32.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-32.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-32.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-32.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-33.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-33.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-33.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-33.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-34.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-34.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-34.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-34.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-35.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-35.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-35.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-35.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-36.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-36.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-36.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-36.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-37-2nd.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-37-2nd.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-37-2nd.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-37-2nd.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-38.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-38.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-38.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-38.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-39.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-39.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-39.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-39.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-4.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-4.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-4.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-4.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-40.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-40.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-40.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-40.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-41.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-41.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-41.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-41.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-42.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-42.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-42.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-42.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-43.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-43.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-43.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-43.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-44.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-44.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-44.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-44.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-45.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-45.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-45.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-45.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-46.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-46.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-46.pin C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-46.pin MSFragger move pepxml C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\lib\fragpipe-18.0.jar;/C:/Users/Administrator/Downloads/FragPipe-jre-18.0/fragpipe/lib/commons-io-2.11.0.jar com.github.chhh.utils.FileMove --no-err C:\Users\Administrator\Downloads\S22034-Nick-47.pepXML C:\Users\Administrator\Downloads\Fragpipe_Output_jre_26Aug2022_Danve\999\S22034-Nick-47.pepXML MSFragger move pin C:\Users\Administrator\Downloads\FragPipe-jre-18.0\fragpipe\jre\bin\java.exe -cp 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jmcalist avatar Aug 27 '22 20:08 jmcalist

I can't find the whole log or the screenshot. Can you put them in a zip file and reply them in the GitHub?

Thanks,

Fengchao

fcyu avatar Aug 28 '22 14:08 fcyu

Thanks so much, here you are! log_2022-08-27_03-20-25.txt SeeMS error message

jmcalist avatar Aug 28 '22 15:08 jmcalist

I have no idea about your errors. It also looks like the Thermo raw reader couldn't work well on your computer.

As a workaround, you can convert your raw files to mzml files, and then, using them in FragPipe. Here is the tutorial: https://fragpipe.nesvilab.org/docs/tutorial_convert.html

Best,

Fengchao

fcyu avatar Aug 28 '22 15:08 fcyu

Thanks so much! I have converted to mzml with past fragpipe runs and will try that again with this one

Thanks as always for all your assistance!

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From: Fengchao @.> Sent: Sunday, August 28, 2022 11:23:10 AM To: Nesvilab/FragPipe @.> Cc: Jason Mcalister @.>; Author @.> Subject: Re: [Nesvilab/FragPipe] Java or RAM issue? (Issue #809)

CAUTION: This email originated from outside of the University of Guelph. Do not click links or open attachments unless you recognize the sender and know the content is safe. If in doubt, forward suspicious emails to @.***

I have no idea about your errors. It also looks like the Thermo raw reader couldn't work well on your computer.

As a workaround, you can convert your raw files to mzml files, and then, using them in FragPipe. Here is the tutorial: https://fragpipe.nesvilab.org/docs/tutorial_convert.html

Best,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/809#issuecomment-1229484640, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARFTQLIAUGLZ2T4SFN4CSG3V3N755ANCNFSM57X62NPQ. You are receiving this because you authored the thread.Message ID: @.***>

jmcalist avatar Aug 28 '22 15:08 jmcalist