GISTIC2 Issue

[John L Pulice]

Hi all,

GISTIC2 keeps throwing me the following error: /opt/gpcloud/gp_home/taskLib/GISTIC_2.0.6.15.28.796/gp_gistic2_from_seg: error while loading shared libraries: libmwlaunchermain.so: cannot open shared object file: No such file or directory

This occurs on files I successfully ran with GISTIC2 two weeks ago, not sure what has happened since! I am using default settings and just the hg19 or hg38 MAT file. 

Thanks!

John

[Hanie Azari]

I also keep facing this issue, have you found any solution?

best,

hanie A

[tmt...@cloud.ucsd.edu]

Hello John and Hanie,

We recently updated the GISTIC2 module, so it is possible that this indicative that something is wrong with the new version. We'll look into this further.

In the meantime, you can use the older version of the module by clicking on the link below. Let us know if this resolves your issue.

https://cloud.genepattern.org/gp/pages/index.jsf?lsid=urn:lsid:broad.mit.edu:cancer.software.genepattern.module.analysis:00125:6.15.21

Thorin Tabor
GenePattern Team

[Hanie Azari]

Dear Thorin,

 

Thanks for your early response,

I also have overlapped issues in CNVanalysis using GISTIC online, how should I remove it?

Would you please help me with that? I’ve been looking for a solution for weeks

 my file is a CNV of Colon cancer from TCGA which is attached here.

[tmt...@cloud.ucsd.edu]

We have just updated the GISTIC_2.0 module. Please try again.

Thorin Tabor
GenePattern Team

On Friday, February 10, 2023 at 6:43:04 PM UTC-8 jpu...@broadinstitute.org wrote:

[Hanie Azari]

Dear thorin, 

I tried again, but I faced the same problem 

my job number is Job 493067 - GISTIC_2.0

would you please check this problem?

best, 

Hanie A

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[John L Pulice]

My issues were completely resolved, thanks Thorin!!

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John Pulice

PhD Candidate, Program in Biological and Biomedical Sciences, Harvard Medical School

NDSEG Fellow, Meyerson Lab, Dana-Farber Cancer Institute

jpu...@broadinstitute.org – he/him

[tmt...@cloud.ucsd.edu]

Hanie,

This appears to be an error within GISTIC itself, so to understand this error it's best to consult the GISTIC forum (https://groups.google.com/a/broadinstitute.org/g/gistic-forum) where the authors and developers of GISTIC can respond.

Hope this helps!

Thorin Tabor
GenePattern Team

[Hanie Azari]

thanks for your reply thorin 🌹

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