I installed biobakery workflows in a python environment (Installing the workflows with pip · biobakery/biobakery_workflows Wiki · GitHub).
Kneaddata and metaphlan works, but strainfphlan fails. Humann too, but I wil work on it after I fix this.
The main problem is makeblastdb. I have reinstalled blast, phylophlan and metaphlan, but anything worked
2022-02-14 09:46:23,287 LoggerReporter log_event INFO: task 167, strainphlan_clade_0 : ready and waiting for resources
2022-02-14 09:46:23,287 LoggerReporter log_event INFO: task 167, strainphlan_clade_0 : starting to run
2022-02-14 09:46:23,296 anadama2.helpers actually_sh INFO: Executing with shell: extract_markers.py --database /home/microviable/workflows/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.pkl --clade s__Faecalibacterium_prausnitzii --output_dir /media/microviable/e/workflows_output/strainphlan
2022-02-14 09:47:11,311 anadama2.helpers actually_sh INFO: Execution complete. Stdout: b’Mon Feb 14 09:46:23 2022: Start extract markers execution\nMon Feb 14 09:46:23 2022: \tGenerating DB markers FASTA…\nMon Feb 14 09:46:59 2022: \tDone.\nMon Feb 14 09:46:59 2022: \tLoading MetaPhlan 3.0 database…\nMon Feb 14 09:47:04 2022: \tDone.\nMon Feb 14 09:47:04 2022: \tNumber of markers for the clade “s__Faecalibacterium_prausnitzii”: 41\nMon Feb 14 09:47:04 2022: \tExporting markers…\nMon Feb 14 09:47:11 2022: \tDone.\nMon Feb 14 09:47:11 2022: Finish extract markers execution (47.93 seconds): Results are stored at “/media/microviable/e/workflows_output/strainphlan/”\n’
Stderr:
2022-02-14 09:47:11,314 anadama2.helpers actually_sh INFO: Executing with shell: strainphlan --samples /media/microviable/e/workflows_output/strainphlan//.pkl --output_dir /media/microviable/e/workflows_output/strainphlan --clade s__Faecalibacterium_prausnitzii --nprocs 4 --clade_markers /media/microviable/e/workflows_output/strainphlan/s__Faecalibacterium_prausnitzii.fna > /media/microviable/e/workflows_output/strainphlan/19_clade.log && touch /media/microviable/e/workflows_output/strainphlan/19_clade.tree && if [ -f /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Faecalibacterium_prausnitzii.tree ]; then cp /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Faecalibacterium_prausnitzii.tree /media/microviable/e/workflows_output/strainphlan/19_clade.tree; fi
2022-02-14 09:47:12,058 LoggerReporter task_failed ERROR: task 167, strainphlan_clade_0 : Failed! Error message : Error executing action 0. Original Exception:
Traceback (most recent call last):
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in _run_task_locally
action_func(task)
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/tasks/shotgun.py”, line 762, in strainphlan
args=[os.path.abspath(os.path.join(os.path.dirname(task.depends[0].name),"…")),os.path.dirname(task.targets[0].name),profile_clade,threads])
File “/home/microviable/workflows/lib/python3.7/site-packages/biobakery_workflows/utilities.py”, line 1049, in run_task
return_code = sh(command)()
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually_sh
ret = _sh(s, **kwargs)
File “/home/microviable/workflows/lib/python3.7/site-packages/anadama2/util/init.py”, line 320, in sh
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))
anadama2.util.ShellException: [Errno 1] Command `strainphlan --samples /media/microviable/e/workflows_output/strainphlan//.pkl --output_dir /media/microviable/e/workflows_output/strainphlan --clade s__Faecalibacterium_prausnitzii --nprocs 4 --clade_markers /media/microviable/e/workflows_output/strainphlan/s__Faecalibacterium_prausnitzii.fna > /media/microviable/e/workflows_output/strainphlan/19_clade.log && touch /media/microviable/e/workflows_output/strainphlan/19_clade.tree && if [ -f /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Faecalibacterium_prausnitzii.tree ]; then cp /media/microviable/e/workflows_output/strainphlan/RAxML_bestTree.s__Faecalibacterium_prausnitzii.tree /media/microviable/e/workflows_output/strainphlan/19_clade.tree; fi’ failed.
Out: b’’
Err: b’[e] could not find “makeblastdb” (“False”) executable in your PATH environment variable\n\n[e] An error was ocurred executing a external tool, exiting…\nMon Feb 14 09:47:12 2022: Stop StrainPhlAn 3.0 execution.\n’