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.