I am testing the wmgx workflow using demo files and am running into an error. It appears that the error is specific to the script “shotgun.py”
(biobakery_prod) fatimas**@alustt129** PROD$ biobakery_workflows wmgx --input /home/nicoleg/.conda/envs/biobakery_prod/tutorial/input/ --output ~/test-wmgx_prod/Testing_Output_wmgx_demo --local-jobs 2 --bypass-strain-profiling --contaminate-database /home/nicoleg/.conda/envs/biobakery_prod/tutorial/kneaddata_demo_db/
Traceback (most recent call last):
File “/home/nicoleg/.conda/envs/biobakery_prod/bin/wmgx.py”, line 121, in
args.pair_identifier, args.qc_options, args.remove_intermediate_output)
File “/home/fatimas/.local/lib/python3.7/site-packages/biobakery_workflows/tasks/shotgun.py”, line 270, in quality_control
remove_intermediate_output)
File “/home/fatimas/.local/lib/python3.7/site-packages/biobakery_workflows/tasks/shotgun.py”, line 98, in kneaddata
kneaddata_output_folder = os.path.dirname(kneaddata_output_files[0][0])
TypeError: ‘zip’ object is not subscriptable
Any input is appreciated. Thank you