plugin error from phylogeny - no such file or directory: mafft

Hello!

I'm new to the use of Qiime2 and am trying to get the hang of if by following the Moving Pictures Tutorial. This forum has been a great help, so I first wanted to thank all of you already!

The problem I face is at the step where the phylogenetic tree is supposed to be created using the phylogeny plugin. Everything before works fine.
The following code is provided by the Moving Pictures Tutorial:

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences rep-seqs.qza \
  --o-alignment aligned-rep-seqs.qza \
  --o-masked-alignment masked-aligned-rep-seqs.qza \
  --o-tree unrooted-tree.qza \
  --o-rooted-tree rooted-tree.qza

The error message I get is the following:

Plugin error from phylogeny:
  [Errno 2] No such file or directory: 'mafft'
Debug info has been saved to /tmp/qiime2-q2cli-err-ejlhs69e.log

If I run it with the --verbose flag, the error message is:

Running external command line application. This may print messages to stdout and/or stderr.
The command being run is below. This command cannot be manually re-run as it will depend on temporary files that no longer exist.

Command: mafft --preservecase --inputorder --thread 1 /tmp/qiime2/vsc10755/data/beef5cfe-eceb-4076-9708-8be6f6bf8876/data/dna-sequences.fasta

Traceback (most recent call last):
  File "/apps/brussel/CO7/skylake/software/QIIME2/2022.11-foss-2020b/lib/python3.8/site-packages/q2cli/commands.py", line 352, in __call__
    results = action(**arguments)
  File "<decorator-gen-228>", line 2, in align_to_tree_mafft_fasttree
  File "/apps/brussel/CO7/skylake/software/QIIME2/2022.11-foss-2020b/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/apps/brussel/CO7/skylake/software/QIIME2/2022.11-foss-2020b/lib/python3.8/site-packages/qiime2/sdk/action.py", line 475, in _callable_executor_
    outputs = self._callable(scope.ctx, **view_args)
  File "/apps/brussel/CO7/skylake/software/QIIME2/2022.11-foss-2020b/lib/python3.8/site-packages/q2_phylogeny/_align_to_tree_mafft_fasttree.py", line 19, in align_to_tree_mafft_fasttree
    aligned_seq, = mafft(sequences=sequences, n_threads=n_threads,
  File "<decorator-gen-565>", line 2, in mafft
  File "/apps/brussel/CO7/skylake/software/QIIME2/2022.11-foss-2020b/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/apps/brussel/CO7/skylake/software/QIIME2/2022.11-foss-2020b/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/apps/brussel/CO7/skylake/software/QIIME2/2022.11-foss-2020b/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 128, in mafft
    return _mafft(sequences_fp, None, n_threads, parttree, False)
  File "/apps/brussel/CO7/skylake/software/QIIME2/2022.11-foss-2020b/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 100, in _mafft
    run_command(cmd, result_fp)
  File "/apps/brussel/CO7/skylake/software/QIIME2/2022.11-foss-2020b/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 26, in run_command
    subprocess.run(cmd, stdout=output_f, check=True)
  File "/apps/brussel/CO7/skylake/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/subprocess.py", line 489, in run
    with Popen(*popenargs, **kwargs) as process:
  File "/apps/brussel/CO7/skylake/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/subprocess.py", line 854, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "/apps/brussel/CO7/skylake/software/Python/3.8.6-GCCcore-10.2.0/lib/python3.8/subprocess.py", line 1702, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'mafft'

Plugin error from phylogeny:

  [Errno 2] No such file or directory: 'mafft'

See above for debug info.

I've looked for a solution for the problem I'm encountering on the forum, but weirdly enough I don't seem to find cases similar enough to help me.

I'm running the v2022.11 version of qiime installed on the university's server (I don't know how it is installed ...).

HI @fdebus,

I am not noticing anything in the error log that'd help me ascertain what the issue is...

It'd probably be a good idea to contact the IT staff maintaining the University HPC. Perhaps hey might have modified the base QIIME 2 install? This is just a guess, but I wonder why the environment / path is named 2022.11-foss-2020b.

-Mike

Hi Mike,

Thank you for your time and answer!
I'll contact them.

It was indeed a problem in the implementation by the IT staff. They have resolved the issue.

Thank you again for your help!

2 Likes

I'm glad you were able to resolve this, and you for letting us know! :sparkler:

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