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rahulg603 / mtSwirl

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Issue with jsontools.py file #9

Open goharkhan7 opened 1 month ago

goharkhan7 commented 1 month ago

while running the multi sample code i get this error

multi_sam/cromwell-executions/MitochondriaPipeline/f10932f4-93f7-4b3c-8bea-e5c4e2455827/call-AlignAndCallR2/AlignAndCallR2/1887beac-6a1e-457e-8d2c-e25b68b1fa2a/call-AlignToMtRegShiftedAndMetrics/execution/stderr

Upon looking to the stderr file i get the following statements

Traceback (most recent call last): File "/cromwell-executions/MitochondriaPipeline/f10932f4-93f7-4b3c-8bea-e5c4e2455827/call-AlignAndCallR2/AlignAndCallR2/1887beac-6a1e-457e-8d2c-e25b68b1fa2a/call-AlignToMtRegShiftedAndMetrics/inputs/603824970/jsontools.py", line 67, in data_in = parse_vars(args.set, type=str) File "/cromwell-executions/MitochondriaPipeline/f10932f4-93f7-4b3c-8bea-e5c4e2455827/call-AlignAndCallR2/AlignAndCallR2/1887beac-6a1e-457e-8d2c-e25b68b1fa2a/call-AlignToMtRegShiftedAndMetrics/inputs/603824970/jsontools.py", line 31, in parse_vars key, value = parse_var(item) File "/cromwell-executions/MitochondriaPipeline/f10932f4-93f7-4b3c-8bea-e5c4e2455827/call-AlignAndCallR2/AlignAndCallR2/1887beac-6a1e-457e-8d2c-e25b68b1fa2a/call-AlignToMtRegShiftedAndMetrics/inputs/603824970/jsontools.py", line 20, in parse_var return (key, value) UnboundLocalError: local variable 'value' referenced before assignment

The script is running with the default values using cromwell-87 on local machine. Is this issue is inside the jsontools.py file? How to fix this error?

rahulg603 commented 1 month ago

Hello! I believe this issue is due to your use of the multi-sample pipeline, which is incompatible with Cromwell and is intended for the DNANexus RAP platform. Please use the single-sample pipeline – this pipeline analyzes one sample per job but can be parallelized with scatter-gather.