Question: Deseq2 error slurmstepd: error: xcgroup_instantiate: unable to create cgroup '/sys/fs/cgroup/memory/slurm/uid_819800/job_14640588' : No space left on device sl
1
gravatar for trevor.blain
13 days ago by
trevor.blain10
trevor.blain10 wrote:

slurmstepd: error: xcgroup_instantiate: unable to create cgroup '/sys/fs/cgroup/memory/slurm/uid_819800/job_14640588' : No space left on device

I get this error on galaxy when attempting to run Deseq2 on my counts data. Any idea what's causing this?

rna-seq • 142 views
ADD COMMENTlink written 13 days ago by trevor.blain10

This is occurring at https://usegalaxy.org, correct?

ADD REPLYlink written 13 days ago by Jennifer Hillman Jackson25k

Our admin will be looking into this -- it is the only current report of the problem so far.

Please try a re-run for now, maybe a few. We use multiple clusters and only one may be impacted. At least one of those rerun jobs is likely to hit a different cluster. This happens every so often, so if the job was run sometimes earlier, the problem could be related to a prior issue that has since been resolved.

If you can't get a successful job now, please send in a bug report from one of the error datasets for troubleshooting. Please leave all inputs/output undeleted, including the additional reruns. Including a link to this Biostars post in the bug report comments will help to link it the email to this post.

Thanks! Jen, Galaxy team

ADD REPLYlink written 13 days ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 105 users visited in the last hour