The Biowulf profile would complain that the slurm_script had an unbound variable and called it a workflow error even if all the tasks finished successfully.
Email from Dayne about this:
It means it could not find the SLURM variable indicating the job is complete even though the job did complete. A issue will need to be generated. This is specific to ccad2 and how the jobid is displayed.
Acutal Error message from the run
[Fri Sep 15 11:59:36 2023]
Finished job 0.
139 of 139 steps (100%) done
Complete log: /gpfs/gsfs10/users/COVNET_GWAS/wendy/test_1.2.0/.snakemake/log/2023-09-15T101315.752775.snakemake.log
sex_chr_included True
gwas = False
/var/spool/slurm/slurmd/job8172198/slurm_script: line 151: exit_status: unbound variable
################################################################################
# CGR SUBMIT: There was a workflow error, check logs and re-run.
# Exit Code: 1
# End Date: 2023-09-15
# End Time: 11:59:40
################################################################################
The Biowulf profile would complain that the slurm_script had an unbound variable and called it a workflow error even if all the tasks finished successfully.
Email from Dayne about this: It means it could not find the SLURM variable indicating the job is complete even though the job did complete. A issue will need to be generated. This is specific to ccad2 and how the jobid is displayed.
Acutal Error message from the run