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incorporates the latest changes from production testing. #133

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Mar 14, 2024
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13 changes: 10 additions & 3 deletions sequence_processing_pipeline/Job.py
Original file line number Diff line number Diff line change
Expand Up @@ -232,8 +232,11 @@ def submit_job(self, script_path, job_parameters=None,

job_info = {'job_id': None, 'job_name': None, 'job_state': None,
'elapsed_time': None}
# Just to give sometime for everything to be set up properly
sleep(5)
# Just to give some time for everything to be set up properly
sleep(10)

exit_count = 0

while wait:
result = self._system_call(f"sacct -P -n --job {job_id} --format "
"JobID,JobName,State,Elapsed,ExitCode")
Expand Down Expand Up @@ -276,9 +279,13 @@ def submit_job(self, script_path, job_parameters=None,
# if job is completed after having run or exited after having
# run, then stop waiting.
if not set(states) - {'COMPLETED', 'FAILED', 'CANCELLED'}:
# break
exit_count += 1

if exit_count > 4:
break

sleep(5)
sleep(10)

if job_info['job_id'] is not None:
# job was once in the queue
Expand Down
2 changes: 2 additions & 0 deletions sequence_processing_pipeline/templates/nuqc_job.sh
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,8 @@
### as well as sbatch -c. demux threads remains fixed at 1.
### Note -c set to 4 and thread counts set to 7 during testing.
#SBATCH -c {{cores_per_task}}
#SBATCH --gres=node_jobs:4


echo "---------------"
echo "Run details:"
Expand Down
2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -48,4 +48,4 @@
],
entry_points={
'console_scripts': ['demux=sequence_processing_pipeline.scripts.cli'
':demux',], })
':demux', ], })