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User's incorrect configuration resulted in not enough memory crashing FragPipe #1665
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Could you change the Thanks, Fengchao |
I run it only with non-zero value (tried 100 and 128 GB - 128 GB is what we physically have). Should I try auto? |
Your computer may not have 100 GB free memory if the 128 GB is the total size. Could you try 64 and 0? Thanks, Fengchao |
Hi @fcyu , Sorry for the delay with the response - I'm using a shared workstation and it took a little longer to find a slot to try 64 or 0. With 64GB, the outcome is exactly the same - FragPipe crashes with the same error file in the
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I think something was wrong in your command because JVM started with 1 GB memory C:\Users\workstation_user\Desktop\Oleg\FragPipe-jre-22.0\fragpipe\jre\bin\java.exe -jar -Dfile.encoding=UTF-8 -Xmx1G C:\Users\workstation_user\Desktop\Oleg\FragPipe-jre-22.0\fragpipe\lib..\tools\MSFragger-4.1\MSFragger-4.1.jar C:\Users\workstation_user\Desktop\Oleg\LFQ_output_27_percolator_try10\fragger.params .... It seems that you only got 1 GB memory. Best, Fengchao |
I'm using a GUI, so I'm not sure what went wrong. I've tried to start the analysis a few more times and each time -Xmx parameter was different (although much higher, e.g., 75, 116, 106 G). |
Something was messed up. Please double check the FragPipe and system configuration
Best, Fengchao |
Hi there,
I'm trying to run a custom LFQ-offset workflow with Percolator for PSM validation. The problem that FragPipe keep crashing. After the crash workstation got restarted, so I can't save the logfile and I don't know at what step exactly it happens (it takes multiple hours for processing and I'm not sitting all the time in from of the screen). However, after a few attempts there was a error files saved in the bin folder of the FragPipe stating the problem with insufficient memory for the JRE.
I've tried to reduce 'parallelism' in the workflow and I have Python configured for Database splitting but it still keep crashing. Is there anything else I can do to make it work?
P.S. there was no such problem with PeptideProphet or when I trialled the workflow on single MS file.
- Workflow
fragpipe.txt - changed extension from .workflow to .txt, otherwise it can't be attached.
- Error files
hs_err_pid6504.log
hs_err_pid9464.log
hs_err_pid20256.log
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