Dear all,
I ran the following code:
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
and encountered Plugin error from phylogeny:
Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/var/folders/kn/tqt5xfzd4x95jq9s21ymqb1r0000gn/T/qiime2-archive-jxhfwcse/c0185c20-f1a8- 4b77-87a2-024afca7065b/data/dna-sequences.fasta']' returned non-zero exit status 1.
Here is the log. It seems that the process was killed after making distance matrix. I would be most grateful for your help!
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 /var/folders/kn/tqt5xfzd4x95jq9s21ymqb1r0000gn/T/qiime2-archive-jxhfwcse
/c0185c20-f1a8-4b77-87a2-024afca7065b/data/dna-sequences.fasta
inputfile = orig
250374 x 1550 - 1250 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8192 kb->48901 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
Making a distance matrix ..
0)^M 33101 / 250374 (thread 0)/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/bin/mafft: line 2751: 26986 Killed: 9 "$prefix/disttbfast" -q $np
ickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $a
dd2ndhalfarg -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 $oneiterationopt < infi
le > pre 2>> "$progressfile"
Traceback (most recent call last):
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/lib/python3.8/site-packages/q2cli/commands.py", line 329, in
__call__
results = action(**arguments)
File "<decorator-gen-228>", line 2, in align_to_tree_mafft_fasttree
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/lib/python3.8/site-packages/qiime2/sdk/action.py", line 485, in _callable_executor_
outputs = self._callable(scope.ctx, **view_args)
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/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 "<decorator-gen-540>", line 2, in mafft
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self._callable_executor_(scope, callable_args,
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/lib/python3.8/site-packages/qiime2/sdk/action.py", line 391, in _callable_executor_
output_views = self._callable(**view_args)
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 128, in mafft
return _mafft(sequences_fp, None, n_threads, parttree, False)
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 100, in _mafft
run_command(cmd, result_fp)
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 26, in run_command
subprocess.run(cmd, stdout=output_f, check=True)
File "/Users/a_mac/opt/miniconda3/envs/MetONTIIME_env/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/var/folders/kn/tqt5xfzd4x95jq9s21ymqb1r0000gn/T/qiime2-archive-jxhfwcse/c0185c20-f1a8-4b77-87a2-024afca7065b/data/dna-sequences.fasta']' returned non-zero exit status 1.