Dear @thermokarst
I am wondering whether you have found some solution regarding previous discussion? I have also got same type of error while doing alignment which is as follows;
qiime alignment mafft --i-sequences ../rep-seqs-dn-99.qza --o-alignment aligned_mafft-ref-seqs.qza --verbose --p-n-threads 24
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 24 /tmp/qiime2-archive-vclzld9_/74cea942-b3a9-4bc2-9b97-65d7cc42d988/data/dna-sequences.fasta
inputfile = orig
230857 x 580 - 200 d
nthread = 24
stacksize: 8192 kb->45089 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
Making a distance matrix ..
18701 / 230857 (thread 23)/home/bxa015/miniconda3/envs/qiime2-2017.12/bin/mafft: line 2440: 10107 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 "/home/bxa015/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in call
results = action(**arguments)
File "", line 2, in mafft
File "/home/bxa015/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/home/bxa015/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 363, in callable_executor
output_views = self._callable(**view_args)
File "/home/bxa015/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_alignment/_mafft.py", line 61, in mafft
run_command(cmd, aligned_fp)
File "/home/bxa015/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_alignment/mafft.py", line 27, in run_command
subprocess.run(cmd, stdout=output_f, check=True)
File "/home/bxa015/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '24', '/tmp/qiime2-archive-vclzld9/74cea942-b3a9-4bc2-9b97-65d7cc42d988/data/dna-sequences.fasta']' returned non-zero exit status 1
Plugin error from alignment:
Command '['mafft', '--preservecase', '--inputorder', '--thread', '24', '/tmp/qiime2-archive-vclzld9_/74cea942-b3a9-4bc2-9b97-65d7cc42d988/data/dna-sequences.fasta']' returned non-zero exit status 1