CuffDiff Fatal Error: Exit code 139

Question

[yrc0313]

Hi,

I received the following error while attempting to use CuffDiff on Galaxy. Any guidance would be appreciated. Thank you!

Fatal error: Exit code 139 ()
[14:22:43] Loading reference annotation.
Warning: No conditions are replicated, switching to 'blind' dispersion method
[14:22:43] Inspecting maps and determining fragment length distributions.
[14:23:07] Modeling fragment count overdispersion.
> Map Properties:
>   Normalized Map Mass: 2126630.66
>   Raw Map Mass: 2481303.74
>   Fragment Length Distribution: Truncated Gaussian (default)
>                 Default Mean: 200
>              Default Std Dev: 80
> Map Properties:
>   Normalized Map Mass: 2126630.66
>   Raw Map Mass: 1608558.50
>   Fragment Length Distribution: Truncated Gaussian (default)
>                 Default Mean: 200
>              Default Std Dev: 80
[14:24:30] Calculating preliminary abundance estimates
[14:24:30] Testing for differential expression and regulation in locus.
/galaxy-repl/main/jobdir/011/507/11507113/tool_script.sh: line 9: 31716 Segmentation fault      (core dumped) cuffdiff --no-update-check --quiet --FDR=0.05 --num-threads="${GALAXY_SLOTS:-4}" --min-alignment-count=10 --library-norm-method=geometric --dispersion-method=pooled --labels '','' /galaxy-repl/main/files/013/953/dataset_13953361.dat /galaxy-repl/main/files/013/952/dataset_13952308.dat /galaxy-repl/main/files/013/952/dataset_13952398.dat

Answer 1

[Devon Ryan]

You'll have to ask the server admin. Just click on the "bug report" icon on the job and send him/her/them a message. It's very likely that you just ran out of memory, but the admin might be able to more easily check.