MinPath error with baqlava 0.5 metaphlan 3.1.0 and humann 3.9

Microbial community profiling BAQLaVa
1

Hi,

After numerous tries getting the exact software version to play nicely (along with the correct database) I thought I was getting close until I got a weird MinPath error trying to run the demo.fq with baqlava 0.5:

(baqlava) [danielsg@c-11-09 examples]$ baqlava -i demo.fq -o test_dir --nucdb BAQLaVa.V0.5.nucleotide/ --protdb BAQLaVa.V0.5.protein/

Writing temp files to directory: test_dir/demo_temp/

mkdir: cannot create directory ‘test_dir’: File exists
mkdir: cannot create directory ‘test_dir/demo_temp/’: File exists
mkdir: cannot create directory ‘test_dir/demo_baqlava/’: File exists
(Nov 26 14:14:05) [ 0/10 -   0.00%] **Ready    ** Task  0: Running HUMAnN to depete bacterial reads from file
(Nov 26 14:14:05) [ 0/10 -   0.00%] **Started  ** Task  0: Running HUMAnN to depete bacterial reads from file
(Nov 26 14:33:49) [ 1/10 -  10.00%] **Failed   ** Task  0: Running HUMAnN to depete bacterial reads from file
(Nov 26 14:33:49) [ 2/10 -  20.00%] **Failed   ** Task  2: Formatting bacterially depleted FASTA file
(Nov 26 14:33:49) [ 3/10 -  30.00%] **Failed   ** Task  3: Running BAQLaVa Nucleotide Search
(Nov 26 14:33:49) [ 4/10 -  40.00%] **Failed   ** Task  7: Running BAQLaVa Translated Search
(Nov 26 14:33:49) [ 5/10 -  50.00%] **Failed   ** Task  4: mv
(Nov 26 14:33:49) [ 6/10 -  60.00%] **Failed   ** Task  5: Calculating Marker Coverage & Abundance
(Nov 26 14:33:49) [ 7/10 -  70.00%] **Failed   ** Task  6: mv
(Nov 26 14:33:49) [ 8/10 -  80.00%] **Failed   ** Task  8: Making BAQLaVa Viral Profile
(Nov 26 14:33:49) [ 9/10 -  90.00%] **Failed   ** Task  9: rm
(Nov 26 14:33:49) [10/10 - 100.00%] **Failed   ** Task 10: rm
Run Finished
Task 0 failed
  Name: Running HUMAnN to depete bacterial reads from file
  Original error:
  Error executing action 0. Original Exception:
  Traceback (most recent call last):
    File "/home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/anadama2/runners.py", line 200, in _run_task_locally
      action_func(task)
    File "/home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/anadama2/helpers.py", line 107, in actually_sh
      ret = _sh(s, **kwargs)
    File "/home/danielsg/miniconda3/envs/baqlava/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 /mnt/isilon/hvp/git_repos/baqlava/examples/demo.fq --output test_dir/demo_temp/ --bypass-translated-search --threads 1' failed.
  Out: Output files will be written to: /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp

  Running metaphlan ........

  Found g__Bacteroides.s__Bacteroides_ovatus : 66.93% of mapped reads
  Found g__Bacteroides.s__Bacteroides_sp_CAG_927 : 33.07% of mapped reads

  Total species selected from prescreen: 2

  Selected species explain 100.00% of predicted community composition


  Creating custom ChocoPhlAn database ........


  Running bowtie2-build ........


  Running bowtie2 ........

  Total bugs from nucleotide alignment: 2
  g__Bacteroides.s__Bacteroides_ovatus: 80531 hits
  g__Bacteroides.s__Bacteroides_sp_CAG_927: 23025 hits

  Total gene families from nucleotide alignment: 2383

  Unaligned reads after nucleotide alignment: 32.3172246114 %

  Bypass translated search

  Computing gene families ...

  Computing pathways abundance and coverage ...

  Err: Error when running glpsol from MinPath.

  Error when running glpsol from MinPath.

  Error when running glpsol from MinPath.


  CRITICAL ERROR: Unable to process all thread commands.

  Error message returned from command for thread task 0: /home/danielsg/miniconda3/envs/baqlava/bin/python3.10 /home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/humann/quantify/MinPath12hmp.py -any /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmp3avj39o1 -map /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpb2jogbps -report /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpl2cye0w1 -details /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpljc3n6mf -mps /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmp5phidr60

  Error message returned from command for thread task 1: /home/danielsg/miniconda3/envs/baqlava/bin/python3.10 /home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/humann/quantify/MinPath12hmp.py -any /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmp_fxenwus -map /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpb2jogbps -report /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmp5w5ekg8h -details /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmplhklxatd -mps /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpim9v07dw

  Error message returned from command for thread task 2: /home/danielsg/miniconda3/envs/baqlava/bin/python3.10 /home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/humann/quantify/MinPath12hmp.py -any /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpiww7_5q8 -map /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpb2jogbps -report /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpi_kvv3o9 -details /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpryqoj965 -mps /mnt/isilon/hvp/git_repos/baqlava/examples/test_dir/demo_temp/demo_humann_temp/tmpsogvaszo/tmpc73ny9e6



Task 2 failed
  Name: Formatting bacterially depleted FASTA file
  Original error:
  Task failed because parent task `0' failed
Task 3 failed
  Name: Running BAQLaVa Nucleotide Search
  Original error:
  Task failed because parent task `2' failed
Task 7 failed
  Name: Running BAQLaVa Translated Search
  Original error:
  Task failed because parent task `2' failed
Task 4 failed
  Name: Task4
  Original error:
  Task failed because parent task `3' failed
Task 5 failed
  Name: Calculating Marker Coverage & Abundance
  Original error:
  Task failed because parent task `2' failed
Task 6 failed
  Name: Task6
  Original error:
  Task failed because parent task `4' failed
Task 8 failed
  Name: Making BAQLaVa Viral Profile
  Original error:
  Task failed because parent task `4' failed
Task 9 failed
  Name: Task9
  Original error:
  Task failed because parent task `8' failed
Task 10 failed
  Name: Task10
  Original error:
  Task failed because parent task `8' failed
Traceback (most recent call last):
  File "/home/danielsg/miniconda3/envs/baqlava/bin/baqlava", line 7, in <module>
    sys.exit(main())
  File "/home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/baqlava/baqlava.py", line 422, in main
    workflow.go()
  File "/home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/anadama2/workflow.py", line 804, in go
    self._handle_finished()
  File "/home/danielsg/miniconda3/envs/baqlava/lib/python3.10/site-packages/anadama2/workflow.py", line 836, in _handle_finished
    raise RunFailed()
anadama2.workflow.RunFailed

Any help would be appreciated. Thanks.

2

After some more searching in the forum, I found out this was due to the humann install. The fix was to:

pip uninstall humann
pip cache purge
pip install humann --no-binary :all:

See the post here for more info

1 Like
3

Hi Scott! Thank you for the update and we are glad to hear this was able to be resolved.