Error using StringTie

Question

[dabs17]

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"

Answer 1

[Devon Ryan]

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.

[dabs17]

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.

[Devon Ryan]

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

[dabs17]

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.