Open Carldeboer opened 1 month ago
Are you able to use the conda profile? These problems are caused by the way apptainer is set up on your cluster - perhaps your cluster admins can help.
The error
container creation failed: image driver mount failure: image driver squashfuse_ll instance exited with error: squashfuse_ll exited: fusermount: mountpoint /dev/fuse is not a directory or a regular file
Seems to be related to this issue. Can you suggest a minimal apptainer command that would be able to reproduce the error directly?
In the mean time I will try the conda profile.
/arc/project/st-cdeboer-1/cdeboer/AFib/Laksman_biobank/work/6c/e7f9e4905b61e1f67635c5d9a607ac/.command.run
will contain a bash script generated by Nextflow for the failing process. The nxf_launch()
function should contain the apptainer command that's failing, which might be enough for a minimal reproducible example. Good luck!
Description of the bug
Still trying to get --run_ancestry working, now encountering a new error during plink command execution:
Command used and terminal output
Relevant files
System information
N E X T F L O W ~ version 24.04.2 HPC local singularity linux pgsc_calc v2.0.0-beta-gba5d0f8