Hi,
I was hoping a could use some help to solve an issue I’m facing while running a Nextflow workflow. I’m running Trim Galore within the workflow, and the process consistently freezes when the logs indicate:
“xxx,xxx,xxx reads processed”
(The number of reads processed varies each time.) However, it doesn’t throw any errors or stop running—unless I manually terminate it. The .nextflow.log still shows the process as “RUNNING”, but no further progress occurs. We’re currently transitioning to a new job scheduler, so at the moment, the job is being run as a foreground process, within a screen session. Additionally, to add to the confusion, the workflow ran successfully to completion on 12 samples, but started “hanging” when I scaled up to 25 samples.
Has anyone encountered similar behavior in Nextflow? Any insights on what might be causing this or how to troubleshoot it?
Thanks in advance for your help!
Monica
