# Biobakery wmgx\_wmtx

**URL:** <https://forum.biobakery.org/t/biobakery-wmgx-wmtx/8693>\
**Category:** bioBakery workflows\
**Created:** [December 19, 2025, 8:56am UTC](https://forum.biobakery.org/t/biobakery-wmgx-wmtx/8693 "2025-12-19T08:56:19Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![LEEzhu0110](https://avatars.discourse-cdn.com/v4/letter/l/e8c25b/32.png) [@LEEzhu0110](https://forum.biobakery.org/u/LEEzhu0110)\
**Post date:** [December 19, 2025, 8:56am UTC](https://forum.biobakery.org/t/biobakery-wmgx-wmtx/8693/1 "2025-12-19T08:56:19Z")

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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!