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CCBR / RENEE

A comprehensive quality-control and quantification RNA-seq pipeline
https://CCBR.github.io/RENEE/
MIT License
3 stars 4 forks source link

error running jobby #155

Closed kelly-sovacool closed 1 month ago

kelly-sovacool commented 1 month ago 
run_jobby_on_snakemake_log logfiles/snakemake.log | tee logfiles/snakemake.log.jobby | cut -f2,3,18 > logfiles/snakemake.log.jobby.short
bash: /data/CCBR_Pipeliner/db/PipeDB/Conda/envs/py311/bin/run_jobby_on_snakemake_log: Permission denied
CalledProcessError in file /data/CCBR/projects/ccbr1358/renee_mm10_M25_20240820/workflow/Snakefile, line 241:
Command 'set -euo pipefail;  run_jobby_on_snakemake_log logfiles/snakemake.log | tee logfiles/snakemake.log.jobby | cut -f2,3,18 > logfiles/snakemake.log.jobby.short' returned non-zero exit status 126.
  File "/data/CCBR/projects/ccbr1358/renee_mm10_M25_20240820/workflow/Snakefile", line 241, in __onsuccess
OnSuccess
run_jobby_on_snakemake_log logfiles/snakemake.log | tee logfiles/snakemake.log.jobby | cut -f2,3,18 > logfiles/snakemake.log.jobby.short

jobby failed for @TJoshMeyer within the snakemake worfklow, but works fine when he runs it interactively

kelly-sovacool commented 1 month ago

There seems to be a jobby in the conda env in addition to the one we make available in the ccbrpipeliner module. The one in conda throws this error, while the one in the module works.

kelly-sovacool commented 1 month ago

I removed the jobby scripts in the conda env. Running a test now, output in /data/sovacoolkl/renee_test_latest/

kelly-sovacool commented 1 month ago

fixed by removing them from the conda env, since we are making them available in the ccbrpipeliner module now