Path output alpha-analysis.sif

[JtheBAB]

Hi

When we run alpha-analysis.sif

apptainer exec --no-home --bind /mnt/group/data01/user/AF_pulldown_E3/experiment_4:/mnt /mnt/group/data01/user/alpha-analysis.sif run_get_good_pae.sh --output_dir=/mnt --cutoff=15

it runs as expected but creates within /mnt/group/data01/user/AF_pulldown_E3/experiment_4 again the full path /mnt/group/data01/user/AF_pulldown_E3/experiment_4. How can we avoid this?

Best wishes

[dingquanyu]

Hi @JtheBAB

Sorry I didn't see this sort of behaviour when using singularity exec. I guess apptainer might have some settings that are different from singularity? I'm not familiar with apptainer though.

Yours
Dingquan

[JtheBAB]

Hi Dingquan

As far as i understand apptainer is just singularity.

https://apptainer.org/news/community-announcement-20211130/

Maybe a version thing?

We have 1.3.0-1.el8

Best wishes

[dingquanyu]

Hi,

I see. I've been using version 1.2.5-1.el8. I'm not sure whether it's caused by different versions.
Yours
Dingquan