phylogeny plugin error

Hi,

I run same command on different file did not give error but now showing error: Is there any issue with input file?

$ 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 --verbose
    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-yj89xyr5/0d758925-d39f-4c0c-8ab0-f993e5f5d64c/data/dna-sequences.fasta


inputfile = orig
63154 x 388 - 215 d
nthread = 1
stacksize: 8192 kb->12334 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..
 34401 / 63154 (thread    0)/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/bin/mafft: line 2440: 12130 Killed                  "$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > pre 2>> "$progressfile"
Traceback (most recent call last):
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2cli/commands.py", line 311, in __call__
    results = action(**arguments)
  File "</opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/decorator.py:decorator-gen-226>", line 2, in align_to_tree_mafft_fasttree
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
    output_types, provenance)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py", line 458, in _callable_executor_
    outputs = self._callable(scope.ctx, **view_args)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2_phylogeny/_align_to_tree_mafft_fasttree.py", line 18, in align_to_tree_mafft_fasttree
    aligned_seq, = mafft(sequences=sequences, n_threads=n_threads)
  File "</opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/decorator.py:decorator-gen-479>", line 2, in mafft
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
    output_types, provenance)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 85, in mafft
    run_command(cmd, aligned_fp)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 27, in run_command
    subprocess.run(cmd, stdout=output_f, check=True)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-yj89xyr5/0d758925-d39f-4c0c-8ab0-f993e5f5d64c/data/dna-sequences.fasta']' returned non-zero exit status 1.

Plugin error from phylogeny:

  Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-yj89xyr5/0d758925-d39f-4c0c-8ab0-f993e5f5d64c/data/dna-sequences.fasta']' returned non-zero exit status 1.

See above for debug info.

thanks

4 posts were merged into an existing topic: Plugin error from dada2:R and Traceback

Hi,

I run same command on different file did not give error but now showing error: Is there any issue with input file?

$ 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 --verbose
    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-yj89xyr5/0d758925-d39f-4c0c-8ab0-f993e5f5d64c/data/dna-sequences.fasta


inputfile = orig
63154 x 388 - 215 d
nthread = 1
stacksize: 8192 kb->12334 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00



Making a distance matrix ..
 34401 / 63154 (thread    0)/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/bin/mafft: line 2440: 12130 Killed                  "$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof $param_fft $algopt $treealg $scoreoutarg < infile > pre 2>> "$progressfile"
Traceback (most recent call last):
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2cli/commands.py", line 311, in __call__
    results = action(**arguments)
  File "</opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/decorator.py:decorator-gen-226>", line 2, in align_to_tree_mafft_fasttree
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
    output_types, provenance)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py", line 458, in _callable_executor_
    outputs = self._callable(scope.ctx, **view_args)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2_phylogeny/_align_to_tree_mafft_fasttree.py", line 18, in align_to_tree_mafft_fasttree
    aligned_seq, = mafft(sequences=sequences, n_threads=n_threads)
  File "</opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/decorator.py:decorator-gen-479>", line 2, in mafft
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
    output_types, provenance)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in _callable_executor_
    output_views = self._callable(**view_args)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 85, in mafft
    run_command(cmd, aligned_fp)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/site-packages/q2_alignment/_mafft.py", line 27, in run_command
    subprocess.run(cmd, stdout=output_f, check=True)
  File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/lib/python3.6/subprocess.py", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-yj89xyr5/0d758925-d39f-4c0c-8ab0-f993e5f5d64c/data/dna-sequences.fasta']' returned non-zero exit status 1.

Plugin error from phylogeny:

  Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-yj89xyr5/0d758925-d39f-4c0c-8ab0-f993e5f5d64c/data/dna-sequences.fasta']' returned non-zero exit status 1.

See above for debug info.

thanks

Good afternoon,

Nope! Here is the error:
34401 / 63154 (thread 0)/opt/gridware/depots/54e7fb3c/el7/pkg/apps/qiime2/2019.4.0/bin/bin/mafft: line 2440: 12130 Killed

This means that the process was ‘killed’ (which means ‘canceled’) by the computer. Try running it again and it could work.

If this command keeps getting killed, post again and we can try to find out why. :+1:

Colin

Hi @colinbrislawn,

Thanks, I again run the same command as script on HPC and it works perfectly.

Thanks
Yogesh

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A post was merged into an existing topic: Plugin error from dada2:R and Traceback