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v_simple of MASH module not recognizing the container

Open hsun3163 opened this issue 2 years ago • 6 comments

while running:

nohup sos run pipeline/mashr.ipynb mash \
    --container containers/stephenslab.sif \
    --output_prefix Ast_Exc_Inh_Mic_OPC_Oli \
    --data output/Ast_Exc_Inh_Mic_OPC_Oli.rds \
    -s force -J 20 -q csg -c csg.yml --cwd MASH_6_celltypes

Following error occurs:

ERROR: [vhat_simple (/mnt/vast/hpc/csg/snuc_pseu]: [0]: Executing script in Singularity returns an error (exitcode=255, stderr=/mnt/vast/hpc/csg/snuc_pseudo_bulk/eight_celltypes_analysis/MASH/MASH_6_celltypes/Ast_Exc_Inh_Mic_OPC_Oli.EZ.V_simple.stderr).
The script has been saved to /home/hs3163/.sos/865d80eff1b4b415/singularity_run_45740.R. To reproduce the error please run:
singularity exec  /home/hs3163/.sos/singularity/library/containers/stephenslab.sif Rscript /home/hs3163/.sos/865d80eff1b4b415/singularity_run_45740.R
[mash]: Exits with 3 pending steps (mash_1, mash_2, prior)

FATAL:   could not open image /home/hs3163/.sos/singularity/library/containers/stephenslab.sif: failed to retrieve path for /home/hs3163/.sos/singularity/library/containers/stephenslab.sif: lstat /mnt/mfs/hgrcgrid/homes/hs3163/.sos/singularity/library/containers: no such file or directory

The problem happened because the vhat_simple step use the wrong path for the singularity image, exemplified by singularity exec /home/hs3163/.sos/singularity/library/containers/stephenslab.sif . However, this problem didn't occur in other steps.

hsun3163 avatar Jul 26 '22 18:07 hsun3163