Strainohlan problem inside biobakery workflows

Infrastructure and utilities bioBakery workflows
1

I ran biobakery workflows and, now I increased RAM to 64GB and Swap memory to the same amount, it finally worked, but I received this error whe strainphlan tries to run strainphlan_clade_XX tasks.

By default, at most ten species identified in the set of samples are profiled by strainphlan inside workflows. The RAxML files contain the trees generated for each species.

Err: b’Traceback (most recent call last):\n File “/home/microviable/workflows/bin/extract_markers.py”, line 8, in \n sys.exit(main())\n File “/home/microviable/workflows/lib/python3.7/site-packages/metaphlan/utils/extract_markers.py”, line 135, in main\n extract_markers(args.database, args.clade, args.output_dir)\n File “/home/microviable/workflows/lib/python3.7/site-packages/metaphlan/utils/extract_markers.py”, line 118, in extract_markers\n os.remove(fasta_markers)\nFileNotFoundError: [Errno 2] No such file or directory: '/media/microviable/f/ELDERLY/strainphlan/db_markers.fna'\n’

2

I install other dependencies (trimal, RAxML, FastTreeMP and ASTRAL) and reinstall PhyloPhlAn runing “phylophlan_write_default_configs.sh” and I almast achieve 100% Biobakery Workflows functionality. Now I have problemms in final clades:

Task 354 failed
  Name: strainphlan_clade_17
  Original error: 
  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/f/GutaliveZimo/strainphlan/*/*.pkl --output_dir /media/microviable/f/GutaliveZimo/strainphlan --clade s__Ruminococcus_bicirculans --nprocs 4  --clade_markers /media/microviable/f/GutaliveZimo/strainphlan/s__Ruminococcus_bicirculans.fna > /media/microviable/f/GutaliveZimo/strainphlan/16_clade.log && touch /media/microviable/f/GutaliveZimo/strainphlan/16_clade.tree && if [ -f /media/microviable/f/GutaliveZimo/strainphlan/RAxML_bestTree.s__Ruminococcus_bicirculans.tree ]; then cp /media/microviable/f/GutaliveZimo/strainphlan/RAxML_bestTree.s__Ruminococcus_bicirculans.tree /media/microviable/f/GutaliveZimo/strainphlan/16_clade.tree; fi' failed. 
  Out: b''
  Err: b'\n[e] Parallel execution fails: string indices must be integers\nTue Oct 18 13:04:11 2022: Stop StrainPhlAn 3.0 execution.\n'

¿Any idea?