SLRUM Script question for batch processing

Asked Sep 11 '22 at 13:21

Active Sep 11 '22 at 13:21

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I am trying to reproduce a bioinformatics workflow hosted at https://bioinformaticsworkbook.org/dataAnalysis/VariantCalling/freebayes-dnaseq-workflow.html#gsc.tab=0

In step 1 of the workflow, I have made the commands and saved them to a file, bwa.cmds. The net next step of instructions says to make the following SLRUM scripts and submit.

makeSLURMs.py 1 bwa.cmds for sub in *.sub; do sbatch $sub; done

I tried to type them on command line or saved them to a .sh file and execute it, but was not succcessdul. Could you please help with clarifying this step Do I need to load a specific module or simply run it as a python script? Thank you, Regards, GSA

asked Sep 11 '22 at 13:21

GSA

_Specifically_, what does "not succcessdul" mean? – ChrisGPT was on strike Sep 11 '22 at 22:56
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. – Community Sep 11 '22 at 22:56

SLRUM Script question for batch processing

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