Dear @Pauline.Sararols
The issue is that the directory scratch in your home directory is a symlink and that it targets a place not mounted. And in your case, your home directory is already mounted at the same location. If I specify an alternate location it works
(baobab)-[sararols@login2 Mut2]$ singularity exec --bind /home/users/s/sararols/scratch:/tmp/bla /home/users/s/sararols/scratch/deepvariant.simg bash
Singularity> ls /tmp/bla/TP_WES/Toy_dataset/Mutations/Mut2/Mut2ab_proband_final.bam
/tmp/bla/TP_WES/Toy_dataset/Mutations/Mut2/Mut2ab_proband_final.bam
and the .bam file is found.
If you don’t specify a bind option, the issue is that the symlink target a place not available from Singularity by default. If you add your scratch in the bind, it works and the symlink inside Singularity correctly resolves to the scratch space.
(baobab)-[sararols@login2 Mut2]$ singularity exec --bind /srv/beegfs/scratch/users/s/sararols/ /home/users/s/sararols/scratch/deepvariant.simg bash
Singularity> ls -la /home/users/s/sararols/scratch/TP_WES/Toy_dataset/Mutations/Mut2/Mut2ab_proband_final.bam
-rw-r--r-- 1 sararols hpc_users 377023952 Jul 14 14:50 /home/users/s/sararols/scratch/TP_WES/Toy_dataset/Mutations/Mut2/Mut2ab_proband_final.bam