Hello,Dear Developer!
I encountered a bug when running Biobakery:
biobakery_workflows wmgx_wmtx --input-metagenome MGX/ --input-metatranscriptome MTX/ --input-mapping mapping.tsv -o /public/agis/zhangyancong_group/lizhu/project/pig2.0/mtxout/ --bypass-norm-ratio --bypass-quality-control --bypass-strain-profiling --grid-jobs 8 --grid slurm --threads 20 --grid-partition low --dry-run > mtx.txt
Traceback (most recent call last):
File “/public/agis/zhangyancong_group/zhangyancong/Lab/tools/Miniconda3/envs/biobakery_workflows/bin/wmgx_wmtx.py”, line 83, in
wms_taxonomic_profile, wms_taxonomy_tsv_files, wms_taxonomy_sam_files = shotgun.taxonomic_profile(workflow,
File “/public/agis/zhangyancong_group/zhangyancong/Lab/tools/Miniconda3/envs/biobakery_workflows/lib/python3.10/site-packages/biobakery_workflows/tasks/shotgun.py”, line 349, in taxonomic_profile
workflow.add_task_gridable(
File “/public/agis/zhangyancong_group/zhangyancong/Lab/tools/Miniconda3/envs/biobakery_workflows/lib/python3.10/site-packages/anadama2/workflow.py”, line 662, in add_task_gridable
self._get_grid().add_task(t, **gridopts)
File “/public/agis/zhangyancong_group/zhangyancong/Lab/tools/Miniconda3/envs/biobakery_workflows/lib/python3.10/site-packages/anadama2/workflow.py”, line 174, in _get_grid
if self.vars.get(“output”) in self.vars.get(“input”):
TypeError: argument of type ‘NoneType’ is not iterable
It was discovered that the issue was caused by adding “–grid-jobs”. After I removed this parameter, everything returned to normal.I am very confused about this because there was no problem when I was running the “wmgx”.The version of the biobakery_workflows wmgx_wmtx that I am using is “wmgx_wmtx.py v3.1”.
I’m very sorry for the inconvenience caused. Please take the time to review my message.
Best wishes!