HISAT2 job has been actively running for 6 days

Hi all,

My HISAT2 on a ca. 20gb dataset has been running (actively running=orange/yellow) for 6 days now.
Is this normal? Should I just wait or kill and re-start the job? Thanks!

Best,
twg

Hi @twg

If a job is still executing, it is usually best to allow it to complete. Deleting and rerunning puts that new job back at the end of the queue. The only reason to rerun is if you already know that the inputs/parameters need to be changed for some reason.

Jobs queue first then execute at all servers. Some servers will attempt to rerun jobs (at a different or larger cluster) if they fail the first run for detectable resource reasons.

20 GB of data (compressed paired end reads?) is around the largest that can be successfully processed at the public sites.

Iā€™m guessing that you are working at UseGalaxy.eu? (The job would have timed out already at UseGalaxy.org, and probably at UseGalaxy.org.au too.) The EU server will attempt a rerun by itself, and they also had some issues over the weekend/yesterday and the server admins may have rerun jobs automatically as part of that fix. So, try to let the job complete. One option would be to start up another job ā€“ with the same inputs/settings ā€“ and letting it run at the same time as the first job. If both happen to succeed, then delete/purge one of the copies.

Hi @jennaj,

Thanks for this answer! I am actually using UseGalaxy.org. So far, it still shows the job as actively running (no time out yet). I will let it continue for now and we will see what happens I guess. Thanks again!

Best