Plugin error from phylogeny: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1' returned non-zero exit status 1.

Hello,

I am experiencing the following error (below) when running the following command (below). I tried this command on multiple cloud instances with high specs, and I have tried running the artifact on the latest version of QIIME 2 after initially trying this on version QIIME2_2019.10. I even tried filtering the representative sequences from a filtered table to make the input less complex. Although I see other posts with similar questions, I am unable to tell if my error output is indicative of the other ones who have received similar error. Your thoughts and advice are much appreciated.

command
*qiime phylogeny align-to-tree-mafft-fasttree *

  • --i-sequences /home/user/work/filtered-single-end-demux_feature_data.qza *
  • --output-dir Fungitree*

error:
Plugin error from phylogeny:

  • Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2/user/data/5f74deaa-5ca6-48a2-9515-7664612a78dc/data/dna-sequences.fasta']' returned non-zero exit status 1.*

error log:
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/user/data/5f74deaa-5ca6-48a2-9515-7664612a78dc/data/dna-sequences.fasta

/opt/conda/envs/qiime2-2023.5/bin/mafft: line 2836: 10514 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 "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 473, in call*
  • results = action(*arguments)
  • File "", line 2, in align_to_tree_mafft_fasttree*
  • File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound_callable*
  • outputs = self.callable_executor(*
  • File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 590, in callable_executor*
  • outputs = self._callable(scope.ctx, *view_args)
  • File "/opt/conda/envs/qiime2-2023.5/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 "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/context.py", line 140, in deferred_action*
  • return action_obj._bind(*
  • File "", line 2, in mafft*
  • File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound_callable*
  • outputs = self.callable_executor(*
  • File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 509, in callable_executor*
  • output_views = self._callable(*view_args)
  • File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 128, in mafft*
  • return _mafft(sequences_fp, None, n_threads, parttree, False)*
  • File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 100, in _mafft*
  • run_command(cmd, result_fp)*
  • File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 26, in run_command*
  • subprocess.run(cmd, stdout=output_f, check=True)*
  • File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/subprocess.py", line 516, in run*
  • raise CalledProcessError(retcode, process.args,*
    subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2/user/data/5f74deaa-5ca6-48a2-9515-7664612a78dc/data/dna-sequences.fasta']' returned non-zero exit status 1.

Hello @Andrew_Pais,

Can you run this command with the --verbose flag as well, and post the output here?

Thank you for helping to clarify the problem @colinvwood. I reran the command in a similar environment on the same files as before, but this time with the --verbose flag. Here is the output:

inputfile = orig
991453 x 65 - 32 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb->193643 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00

Making a distance matrix ..
/opt/conda/envs/qiime2-2023.5/bin/mafft: line 2836: 10360 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 "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2cli/commands.py", line 473, in call
results = action(**arguments)
File "", line 2, in align_to_tree_mafft_fasttree
File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound_callable
outputs = self.callable_executor(
File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 590, in callable_executor
outputs = self._callable(scope.ctx, **view_args)
File "/opt/conda/envs/qiime2-2023.5/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 "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/context.py", line 140, in deferred_action
return action_obj._bind(
File "", line 2, in mafft
File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound_callable
outputs = self.callable_executor(
File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py", line 509, in callable_executor
output_views = self._callable(**view_args)
File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 128, in mafft
return _mafft(sequences_fp, None, n_threads, parttree, False)
File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 100, in _mafft
run_command(cmd, result_fp)
File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 26, in run_command
subprocess.run(cmd, stdout=output_f, check=True)
File "/opt/conda/envs/qiime2-2023.5/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2/user/data/5f74deaa-5ca6-48a2-9515-7664612a78dc/data/dna-sequences.fasta']' returned non-zero exit status 1.

Plugin error from phylogeny:

Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2/user/data/5f74deaa-5ca6-48a2-9515-7664612a78dc/data/dna-sequences.fasta']' returned non-zero exit status 1.

See above for debug info.

Hello @Andrew_Pais,

This seems like in could be a memory issue, as a post with a similar error message suggests. Do you know how much memory is available to this process when it runs?

2 Likes

Thank you for sharing that post. After trying the --p-partree option with a more powerful cloud instance, I was finally able to get an output from the command I previously shared.

1 Like

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