GSEAPreranked error message

[eleni]

Hi, I am trying to run a few GSEAPreranked jobs and keep getting the following error:

"Essential container in task exited"

Job ids: 

464096. GSEAPreranked

464094. GSEAPreranked

Thank you,

Eleni

[Anthony Castanza]

Hi Eleni,

"Essential container in task exited" is usually a result of the virtual machine GenePattern is using to run the job running out of memory. I'd suggest going down to the "Job Options" parameters and changing the default job memory from 2Gb to something more like 8Gb.

If you're still having issues after increasing the job memory please let us know

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[eleni]

Hi Anthony, thank you for your response, I have now tried increasing job memory to 8Gb and to more and also tried increasing the jobcpuCount but keep getting the same error.

eg jobIDs 

464165. GSEAPreranked

464168. GSEAPreranked.

Many thanks for your help on this,

Eleni

[Ted Liefeld]

Eleni,

Sorry for the confusion. There was a bad version of the GSEAPreranked module installed just before the weekend.  The GSEA team is working to create a fix.  In the meantime I removed the latest version and you can try again using the older version 7.3.5.

Thanks for your patience,

Ted

To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/7650567e-f929-4d90-b2e3-eab1c31fd593n%40googlegroups.com.

--

Ted Liefeld                                      UC San Diego

Mesirov Lab                                    lie...@ucsd.edu                                
Office 2A24, BRF-II                        858-246-1974

[Ted Liefeld]

Eleni,

A new version (7.3.7) of GSEAPreranked is now available.  This should correct the errors you were seeing earlier.

Please let us know if this solves your problem.

Thanks,

Ted

[myxu.china]

Dear GengPattern team 

 Thanks for your information my errors have been solved

---- Replied Message ----

From	Ted Liefeld<lie...@broadinstitute.org>
Date	09/27/2022 06:14
To	GenePattern Help Forum<genepatt...@googlegroups.com>
Subject	Re: [genepattern-help:2471] GSEAPreranked error message

To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/a0b0b903-9891-4b36-812b-131331de2a8dn%40googlegroups.com.

[Eleni Maniati]

Many thanks, yes it works now both with v7.3.5 and 7.3.7.

Thanks again for looking into it,

Eleni

To view this discussion on the web visit https://groups.google.com/d/msgid/genepattern-help/a0b0b903-9891-4b36-812b-131331de2a8dn%40googlegroups.com.