non-fatal ERROR: BUSCO and GeneMarkST fail

[mariamadrid19]

Hello! I'm trying to use rnaQUAST on my data. When I run rnaquast --test it works perfectly:

Finished: 2023-11-21 21:32:02
Elapsed time: 0:03:24.335269
NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0

Thank you for using rnaQUAST!

But when I run it on my own data, I get this error:

Finished: 2023-11-21 21:25:46
Elapsed time: 0:00:01.313193
NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 2

non-fatal ERRORs:
non-fatal ERROR: run_BUSCO.py failed for transcripts.fasta!
non-fatal ERROR: GeneMarkS-T failed for transcripts.fasta!

Thank you for using rnaQUAST!

when I check the logs they say:
/bin/sh: run_BUSCO.py: command not found
/bin/sh: gmst.pl: command not found

What might be my problem? I am certain I have both BUSCO and GeneMark installed in my server. Thanks a lot!

[andrewprzh]

Dear @mariamadrid19

What might be my problem? I am certain I have both BUSCO and GeneMark installed in my server. Thanks a lot!

Do you have these tools in $PATH? What happens in you type run_BUSCO.py or gmst.pl in your command line?

Best
Andrey