Plugin error from phylogeny qiime2-2022.2

Technical Support
1

I am using qiime2-2022.2
While running the phylogeny,

qiime phylogeny align-to-tree-mafft-fasttree
--i-sequences 1_7b_rep-seqs-dn-99.qza
--output-dir mafft-fasttree-output

We got the error:

Plugin error from phylogeny:

Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-f3ky81av/e27039dd-d3e9-4cb6-897a-c5c564493b06/data/dna-sequences.fasta']' returned non-zero exit status 1.

Debug info has been saved to /tmp/qiime2-q2cli-err-qx61brxu.log

And the tmp file below:

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-archive-f3ky81av/e27039dd-d3e9-4cb6-897a-c5c564493b06/data/dna-sequences.fasta

inputfile = orig
103123 x 551 - 200 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb->20141 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00


Making a distance matrix ..
/home/rahman/miniconda3/envs/qiime2-2022.2/bin/mafft: line 2756:  4535 Killed                  "$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -g $gexp -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg $anchoropt -x $maxanchorseparation $oneiterationopt < infile > pre 2>> "$progressfile"
Traceback (most recent call last):
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2cli/commands.py", line 339, in __call__
    results = action(**arguments)
  File "<decorator-gen-160>", line 2, in align_to_tree_mafft_fasttree
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 485, in _callable_executor_
    outputs = self._callable(scope.ctx, **view_args)
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/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-456>", line 2, in mafft
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    outputs = self._callable_executor_(scope, callable_args,
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 128, in mafft
    return _mafft(sequences_fp, None, n_threads, parttree, False)
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 100, in _mafft
    run_command(cmd, result_fp)
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 26, in run_command
    subprocess.run(cmd, stdout=output_f, check=True)
  File "/home/rahman/miniconda3/envs/qiime2-2022.2/lib/python3.8/subprocess.py", line 516, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-f3ky81av/e27039dd-d3e9-4cb6-897a-c5c564493b06/data/dna-sequences.fasta']' returned non-zero exit status 1.

Any suggestions?

2

Hi @Shaminur,

Welcome back to the :qiime2: forum!

Here is where the error is coming from:

This usually indicates that you've run out of memory on your machine - depending on how you're running QIIME 2 (via a virtual machine, personal laptop, HPC cluster, etc), I'd recommend allocating more memory on your machine/VM (if possible), reaching out to your system administrator to request more memory allocation from them (if you're working on a cluster of some sort), or trying out another machine with more memory.

Here is a related post that discusses a few things to troubleshoot on your end to determine why you've run out of memory that may be helpful as well:

Hope this helps!

Cheers :lizard:

3

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