This is a test version of Biostars. For the public version, visit https://www.biostars.org.
command not found error when runing bismark modules with cluster flow

Hello

I apologize for this stupid question but am at a lost regarding this one:

I am attempting to use cluster flow in order to streamline multiple bismark sessions that I want to run.

When I try to run the bismark pipeline it launches the appropriate qsub jobs, but when the jobs finish no files are generated.

When I inspect the error files they contain the error:

/state/partition1/apps/local/clusterflow-0.1/modules/bismark_align.cfmod: Command not found.

(and similar errors for all other modules in the pipeline).

I have inspected the modules directory, the files are all there and have an execution premission for all users.

What might be the problem?

Thanks in advance

Dolev Rahat

clusterflow
• 2,507 views • link
updated by Ram Ram • written by dolevrahat • dolevrahat

Can the nodes see that path? I assume you checked on the login node.

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

What Devon said. Ensure you have the appropriate module load or export PATH statement in the beginning of your script.

• 0 views • link
written by Ram Ram

Hi dolevrahat, please provide feedback on members' comments.

• 0 views • link
written by Ram Ram

0 answers

No answers yet.

Log in to answer this question.

More posts like this