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biobakery / biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
http://huttenhower.sph.harvard.edu/biobakery_workflows
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ValueError: Unable to find binary or script `metaphlan' #31

Closed samd1993 closed 1 year ago

samd1993 commented 1 year ago

Hi all,

I am trying to run the biobakery workflow and run into this issue:

(base) (squirrel) [arh0899@qhimem0014 ~]$ biobakery_workflows wmgx --input ~/Saimiri_shotgun --output ~/squirrel/biobakery_workflow
Traceback (most recent call last):
  File "/home/arh0899/squirrel/bin/wmgx.py", line 132, in <module>
    merged_taxonomic_profile, taxonomy_tsv_files, taxonomy_sam_files = shotgun.taxonomic_profile(workflow,
  File "/home/arh0899/squirrel/lib/python3.9/site-packages/biobakery_workflows/tasks/shotgun.py", line 350, in taxonomic_profile
    depends=[depend_fastq,TrackedExecutable("metaphlan")],
  File "/home/arh0899/squirrel/lib/python3.9/site-packages/anadama2/tracked.py", line 199, in __new__
    real_key = cls.key(key)
  File "/home/arh0899/squirrel/lib/python3.9/site-packages/anadama2/tracked.py", line 689, in key
    raise ValueError(
ValueError: Unable to find binary or script `metaphlan'

Any idea what it could be? Thank you!

github-actions[bot] commented 1 year ago

Thank you for creating this issue. We currently field issues through our bioBakery Discourse Support Forum. If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.