Hello @thermokarst
Thank you for your reply.
Here is the command and the output of running with --verbose
(qiime2-2018.8) vorthon@DESKTOP-BCB5NP1:~/d/NGS-output-microbiome-view/QIIME2ANALYSIS/testfecescynoF$ qiime alignment mafft \
--i-sequences fiteredTaxonAssignedSeq.qza \
--p-no-parttree \
--p-n-threads 2 \
--o-alignment fiteredTaxonAssignedAlignment.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 2 /tmp/qiime2-archive-9wcqs478/3f68cb7f-a9e8-4e4f-8be8-685d1af4291b/data/dna-sequences.fasta
inputfile = orig
81589 x 251 - 33 d
nthread = 2
stacksize: 8192 kb->15935 kb
Warning: Failed to extend stack size. It's ok in most cases but there may be problems in --pileup and --chainedtree.
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
Making a distance matrix ..
There are 41412 ambiguous characters.
12801 / 81589 (thread 0)/home/vorthon/miniconda3/envs/qiime2-2018.8/bin/mafft: line 2440: 7582 Segmentation fault (core dumped) "$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"
/home/vorthon/miniconda3/envs/qiime2-2018.8/bin/mafft: fork: Invalid argument
Traceback (most recent call last):
File "/home/vorthon/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py", line 274, in call
results = action(**arguments)
File "", line 2, in mafft
File "/home/vorthon/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/vorthon/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 362, in callable_executor
output_views = self._callable(**view_args)
File "/home/vorthon/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_alignment/_mafft.py", line 85, in mafft
run_command(cmd, aligned_fp)
File "/home/vorthon/miniconda3/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_alignment/_mafft.py", line 27, in run_command
subprocess.run(cmd, stdout=output_f, check=True)
File "/home/vorthon/miniconda3/envs/qiime2-2018.8/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '2', '/tmp/qiime2-archive-9wcqs478/3f68cb7f-a9e8-4e4f-8be8-685d1af4291b/data/dna-sequences.fasta']' returned non-zero exit status 254
Plugin error from alignment:
Command '['mafft', '--preservecase', '--inputorder', '--thread', '2', '/tmp/qiime2-archive-9wcqs478/3f68cb7f-a9e8-4e4f-8be8-685d1af4291b/data/dna-sequences.fasta']' returned non-zero exit status 254
See above for debug info.