ablab/rnaquast

non-fatal ERROR: GeneMarkS-T failed

Closed this issue · 1 comments

kgit95 commented

Hi,

When I run rnaquast --test it works perfectly but when I run it with my data it gives the following error.
Elapsed time: 0:00:04.987569
NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 3

non-fatal ERRORs:
non-fatal ERROR: GeneMarkS-T failed for cogent.fake_genome!
non-fatal ERROR: GeneMarkS-T failed for Trinity!
non-fatal ERROR: GeneMarkS-T failed for transcripts!

Thank you for using rnaQUAST!
The command I used to run rnaquast is:
python rnaQUAST.py -c cogent.fake_genome.fasta Trinity.fasta transcripts.fasta -o /rnaquast_out

when I check the GeneMarkS_T.err.log its says: /bin/sh: 1: gmst.pl: not found

Do you have a idea how to fix this?
Thank you.

andrewprzh commented

Hi, sorry for the delay - something was wrong with GitHub notifications.

I seems like rnaQUAST doesn't see you GeneMatkST binary (which is gmst.pl).
GeneMarkST is not in bioconda, so you have to install it manually from http://topaz.gatech.edu/GeneMark/license_download.cgi and specify its folder in $PATH variable.

All the best
Andrey