Hi,
I am learning to use the pipeline wmgx and the pipeline fails on the Humann3 step.
The traceback said:
Task 13 failed
Name: humann____F-0001-1_S41_L001_R1_001.gz
Original error:
Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/jaume/miniconda3/envs/biobakery3/lib/python3.10/site-packages/anadama2/runners.py”, line 200, in _run_task_locally
action_func(task)
File “/home/jaume/miniconda3/envs/biobakery3/lib/python3.10/site-packages/anadama2/helpers.py”, line 107, in actually_sh
ret = _sh(s, **kwargs)
File “/home/jaume/miniconda3/envs/biobakery3/lib/python3.10/site-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0].decode(‘utf-8’), ret[1].decode(‘utf-8’)))
anadama2.util.ShellException: [Errno 1] Command `humann --input /home/jaume/Escritorio/human3/prova_workflow/kneaddata/main/F-0001-1_S41_L001_R1_001.fastq.gz --output /home/jaume/Escritorio/human3/prova_workflow/humann/main --o-log /home/jaume/Escritorio/human3/prova_workflow/humann/main/F-0001-1_S41_L001_R1_001.log --threads 32 --taxonomic-profile /home/jaume/Escritorio/human3/prova_workflow/metaphlan/main/F-0001-1_S41_L001_R1_001_taxonomic_profile.tsv ’ failed.
Out: Output files will be written to: /home/jaume/Escritorio/human3/prova_workflow/humann/main
Decompressing gzipped file …
Err: Traceback (most recent call last):
File “/home/jaume/miniconda3/envs/biobakery3/bin/humann”, line 10, in
sys.exit(main())
File “/home/jaume/miniconda3/envs/biobakery3/lib/python3.10/site-packages/humann/humann.py”, line 979, in main
custom_database = prescreen.create_custom_database(config.nucleotide_database, bug_file)
File “/home/jaume/miniconda3/envs/biobakery3/lib/python3.10/site-packages/humann/search/prescreen.py”, line 215, in create_custom_database
config.metaphlan_v3_db_version+" or “+metaphlan_v4_db_version+” . Please update your version of MetaPhlAn to at least v3.0."
NameError: name ‘metaphlan_v4_db_version’ is not defined
I have installed all databases… I don’t know how I can correct this error.
Any idea?