Singularity on Slurm about emg-viral-pipeline

[indrikwijaya]

hi @hoelzer, thanks for the reply! It's indeed an issue w/ the initial pull and conversion of the Docker image. I've managed to resolve this by building the singularity image separately. Let me close this issue too, thanks!

[hoelzer]

Hey @indrikwijaya, thanks for your interest in the pipeline and so sorry for the late reply.

As a first check: can you in general pull Singularity images to your machine? Can you please try smt like:

HOME_DIR="/home/users/astar/gis/wijayai"
singularity pull  --name ${HOME_DIR}/scratch/virify/microbiomeinformatics-emg-viral-pipeline-python3-v1.img docker://microbiomeinformatics/emg-viral-pipeline-python3:v1

Does this work and generate an image file in the defined --name path?

If that works, can you try to run the nextflow pipeline again but define --cores 1 --max_cores 1 - sometimes on HPC there are issues w/ the initial pull and conversion of Docker --> Singularity images when done in parallel. Once you have the images downloaded, you can just re-use them also w/ more cores to run the pipeline.