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PominovaMS / denovo_benchmarks

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container creation failed: mount hook function failure: mount overlay->/usr/local/var/apptainer/mnt/session/final error: while mounting overlay: can't mount overlay filesystem to /usr/local/var/apptainer/mnt/session/final: invalid argument #12

Closed BioGeek closed 3 weeks ago

BioGeek commented 3 weeks ago

When I run the benchmark locally on a dataset on a vanilla Ubuntu system I get the the following errors:

$ ./run.sh sample_data/PXD004424
Recalculate all algorithm outputs: false
Processing dataset: PXD004424 (sample_data/PXD004424)
sample_data/PXD004424/mgf/151009_exo4_1.mgf
./outputs/PXD004424/casanovo_output.csv
Processing algorithm: casanovo
RUN ALGORITHM
INFO:    squashfuse not found, will not be able to mount SIF or other squashfs files
INFO:    gocryptfs not found, will not be able to use gocryptfs
INFO:    Converting SIF file to temporary sandbox...
INFO:    fuse-overlayfs not found, will not be able to use FUSE overlay
INFO:    Cleaning up image...
FATAL:   container creation failed: mount hook function failure: mount overlay->/usr/local/var/apptainer/mnt/session/final error: while mounting overlay: can't mount overlay filesystem to /usr/local/var/apptainer/mnt/session/final: invalid argument
PominovaMS commented 3 weeks ago

Thank you very much for troubleshooting this and adding the solution to the README. I've merged the PR.

I haven’t encountered this issue when running on HPC, so it wasn’t included in the instructions. Please let me know if there are other steps that would be helpful to add.