search

dieterich-lab / ImmunOMICS

0 stars 1 forks source link

Problem running singularity container #2

Open ADHDrian opened 1 year ago

ADHDrian commented 1 year ago

Hi Amina, I cloned your code on ImmunOMICS, and tried to run sbatch job.sh with the paths changed. Below is the error output:

KeyError in file /beegfs/homes/achan/git/ImmunOMICS/snakefile, line 9:
'path_out'
  File "/beegfs/homes/achan/git/ImmunOMICS/snakefile", line 9, in <module>
srun: error: slurm-c-mk1-1b: task 0: Exited with exit code 1
ERROR  : Unknown image format/type: /home/achan/Data/NUM_CODEX_PLUS/immun2sev_latest.sif
ABORT  : Retval = 255
ERROR  : Unknown image format/type: /home/achan/Data/NUM_CODEX_PLUS/immun2sev_latest.sif
ABORT  : Retval = 255
ERROR  : Unknown image format/type: /home/achan/Data/NUM_CODEX_PLUS/immun2sev_latest.sif
ABORT  : Retval = 255
ERROR  : Unknown image format/type: /home/achan/Data/NUM_CODEX_PLUS/immun2sev_latest.sif
ABORT  : Retval = 255
ERROR  : Unknown image format/type: /home/achan/Data/NUM_CODEX_PLUS/immun2sev_latest.sif
ABORT  : Retval = 255
ERROR  : Unknown image format/type: /home/achan/Data/NUM_CODEX_PLUS/immun2sev_latest.sif
ABORT  : Retval = 255
ERROR  : Unknown image format/type: /home/achan/Data/NUM_CODEX_PLUS/immun2sev_latest.sif
ABORT  : Retval = 255

The sif is downloaded from zenodo. Attached are the snakefile and config-Top5.yml (.txt extension added just to enable upload)

Thanks! Adrian

snakefile.txt config-Top5.yml.txt

AminaLEM commented 1 year ago

Hi Adrian, Please use the path to sif from job.sh... I didn't update zenodo yet. I will do when everything works. Please change only path to output and directory in the singularity command (job.sh). We want to make sure that everything works from my directory, then we will move to clone the repo.