SomaticSniper failed with exit code 139

Posted in Upload your private data by Corey Miles Wed Jun 06 2018 15:32:24 GMT+0000 (Coordinated Universal Time)·2·Viewed 1,290 times

Hello, I am trying to run SomaticSniper and have uploaded a Normal BAM, Tumor BAM and Reference Sequence (.fasta). The run failed with exit code 139. Any ideas on how to fix this? Thank you!
June 7, 2018

Hello Corey,

I am Darko from Seven Bridges Support team.

Based on the provided error message we assume that used FASTA Reference sequence file, has blank lines in it, probably at the end of the file. As there was no secondary file (.FAI) set for the Reference input on the app itself it was always created on the fly and SomaticSniper fails to index FASTAs with blank lines.

We have updated SomaticSniper app in our Public Apps gallery so it will use corresponding index .FAI file in the future. You can update your app or add it (copy) again from Public Apps and we assume your analysis will finish successfully.

Hope this info helps and if you have any questions please let me know.

Best regards,

June 8, 2018

Perfect! The app is running now. I appreciate the help!

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