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 ...).
