Iso-Seq-Single-Cell-Analysis workflow crashing at the SQANTI3 step

[ndrubins]

Hi,

I'm following your Iso-Seq-Single-Cell-Analysis workflow and in step 8. Compare Against Annotation sqanti3_qc.py is producing an error when calling its perl gmst.pl script with this uninformative message: returned non-zero exit status 1.

This happens in the perl gmst.pl script part that's calling the probuild executable with the command:
SQANTI3/utilities/gmst/probuild --par SQANTI3/utilities/gmst/par_1.default --clean_join sequence --seq dedup.5merge.collapsed_corrected.fasta

The dedup.5merge.collapsed_corrected.fasta that probuild is called with was obviously produced by the collapse_isoforms_by_sam.py script and has 5974 sequences.

So I'm wondering if you have any idea and/or a working example that runs past this step which I might be able to use in order to understand what the problem is.

Thanks!

[ndrubins]

Seems to be caused by the "--" in the file name I'm using (I abbreviated it in my issue).