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
