This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error using StringTie

I keep getting the following error with StringTie

Fatal error: Exit code 139 () /galaxy-repl/main/jobdir/015/491/15491531/tool_script.sh: line 9: 24920 Segmentation fault (core dumped) stringtie "/galaxy-repl/main/files/019/398/dataset_19398565.dat" -o "/galaxy-repl/main/files/019/467/dataset_19467838.dat" -p "${GALAXY_SLOTS:-1}" -C "/galaxy-repl/main/files/019/467/dataset_19467839.dat" -G "/galaxy-repl/main/files/019/466/dataset_19466140.dat"

stringtie exit code 139
• 2,646 views • link
updated by Devon Ryan Devon Ryan • written by dabs17 • dabs17

1 answer

My guess is there's either something wrong with the BAM history item or at least one of the GTF files is doesn't match the genome against which you aligned. Please click the bug report on the history item and your Galaxy admin can help.

• 0 views • link
written by Devon Ryan Devon Ryan

I did move the reference genome and HISAT files to a new history. So the history number of the ref genome file is no longer the same. Would that cause a problem? Since I am using a different reference annotation (gtf) file for StringTie.

• 0 views • link
written by dabs17 • dabs17

This history number doesn't matter, most likely you're using a file with the wrong chromosome naming system.

• 0 views • link
written by Devon Ryan Devon Ryan

That shouldn't be the case. I have successfully used the same reference files for TopHat+Cufflinks analysis, and am trying to use HISAT+StringTie now to compare. Unless StringTie has additional requirements for the gtf file compared to cufflinks.

• 0 views • link
written by dabs17 • dabs17

Log in to answer this question.

More posts like this