Open hrydbeck opened 2 months ago
Likely, the nf-core slack is much more suitable for this kind of thing. Here it seems bwa-mem2 starts (but fails? Or just doesn't exit? Not enough information here). It's quite possible you need to dive into the work directory to figure out what happens, possibly rerunning to see.
Your later log lines are possibly unrelated, but there are some notions that would make me wonder whatever the pipeline gets the inputs it expects.
(It's definitely possible to run pipelines on Dardel, including I believe, raredisease. Whatever it makes sense to run it for animals or ancient populations, I can't have an opinion on).
Description of the bug
I am trying to run the pipeline on the HPC PDC-Dardel and get error messages that I am not able to make sense of. I post it here in case you have any tips on how to figure out what is not working, or if I should use another forum for this type of question or maybe just accept that the pipeline can not be run at HPC-Dardel due to shortcomings of the HPC.
This should include the errors:
On Slack-nf-core-HPC: @pontus wrote:
Could be still running but momentarily disappeared from squeue. Or the job finishing but the file system being broken and it couldn't write results/output status. Or the node crashing. Or the job timing out and not succeeding to write any exit code. Or something else. Unless it times out and it manages to make the node stuck, rerunning with
-resume
should be helpful.Command used and terminal output
Relevant files
nextflow.log
System information
version 23.10.1 HPC slurm Singularity dev