Hi,
I'm working on a HPC, and switch to a new clus...
# nf-testl
Louis Le Nézet
03/04/2026, 9:53 AMHi,
I'm working on a HPC, and switch to a new cluster, but I'm now getting
> FATAL: while opening capability config file: open /usr/local/etc/singularity/capability.json: permission deniedLouis Le Nézet
03/04/2026, 10:24 AMWhat's strange is that I'm working on two server sharing the same storage.
On one everything works, normally, and on the other one I'm getting this error.
Louis Le Nézet
03/04/2026, 11:20 AMAfter installing instead singularity in my conda environment
I'm now getting
Copy code
> FATAL: while extracting /WORKING_DIRECTORY/llenezet/phaseimpute/.nf-test/tests/ad2bdccd1711c997a1ed90cdd653442b/work/singularity/depot.galaxyproject.org-singularity-gawk-5.3.0.img: root filesystem extraction failed: extract command failed: ERROR : Failed to create container process: Operation not permittedn
Niklas Schandry
03/04/2026, 2:35 PMOn a new HPC, I would guess that singularity is not properly set up and tries to do things outside of userspace / with root
l
Louis Le Nézet
03/04/2026, 2:37 PMYeah after a lot of debugging it seems that HPC1 had read permission on the
/usr/local/etc/singularity/