`WARNING: underlay of /usr/share/zoneinfo/Etc/UTC required more than 50 (57) bind mounts` about simpli HOT 2 CLOSED

Hi @paulmenzel,

Sorry for the late reply, but I switched jobs, and I am longer working on mantaining/developing SIMPLI.
I think the singularity warning could be a good indication of what's going on, but we would need more info.
What are the contents of /dev/shm/nextflow/work/37/ac837e73cad46da68cc57e2a64ec93 ?
There should be a log file `` with a more descriptive error message. I expect a "File not found" type of error .
The folder should also contain a symlink to a .mcd file with the raw IMC data. If the symlink is broken, then the problem is with the path in the raw IMC metadata file. This is quite unlikely since you are running the example workflow. If the symlink is OK, then it means that singularity can't bind the folder, which could point back to the warning you see.
In the same folder you can also find the `.command.sh` and `.command.run` files which contain the exact commands ran by nextflow in this step.
Hope this helps, if you could post the contents of the `/dev/shm/nextflow/work/37/ac837e73cad46da68cc57e2a64ec93 ` folder and the log file, then I could have a better look into this.
Thank you for bringing up this issue.
Best wishes

Michele

from simpli.

Solved by switching from singularity to apptainer according to this discussion in the nextflow repository.
For the switch to apptainer from singularity see this issue: #8 (comment).

from simpli.