Thank you @Oddant1 !
(base) EB-PTH-J4YXWM37:~ toba1$ cd /Users/toba1/Desktop/Qiime2_test
(base) EB-PTH-J4YXWM37:Qiime2_test toba1$ conda activate qiime2-2023.2
(qiime2-2023.2) EB-PTH-J4YXWM37:Qiime2_test toba1$
(qiime2-2023.2) EB-PTH-J4YXWM37:Qiime2_test toba1$ time qiime alignment mafft \
--i-sequences merged-rep-seqs.qza
--o-alignment aligned-rep-seqs.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 /var/folders/f6/744zv7hn72b8j94jxqfcs5rjrrwhlz/T/qiime2/toba1/data/afd9f936-bdc5-4811-9736-349a4b90933d/data/dna-sequences.fasta
inputfile = orig
231198 x 422 - 200 d
nthread = 1
nthreadpair = 1
nthreadtb = 1
ppenalty_ex = 0
stacksize: 8176 kb->45155 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00
Making a distance matrix ..
231101 / 231198 (thread 0)
done.
/Users/miniconda3/envs/qiime2-2023.2/bin/mafft: line 2836: 10248 Killed: 9 "$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -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 $oneiterationopt < infile > pre 2>> "$progressfile"
Traceback (most recent call last):
File "/Users/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 468, in call
results = action(**arguments)
File "", line 2, in mafft
File "/Users/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 274, in bound_callable
outputs = self.callable_executor(
File "/Users/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 509, in callable_executor
output_views = self._callable(**view_args)
File "/Users/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 128, in mafft
return _mafft(sequences_fp, None, n_threads, parttree, False)
File "/Users/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 100, in _mafft
run_command(cmd, result_fp)
File "/Users/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_alignment/_mafft.py", line 26, in run_command
subprocess.run(cmd, stdout=output_f, check=True)
File "/Users/miniconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/var/folders/f6/744zv7hn72b8j94jxqfcs5rjrrwhlz/T/qiime2/toba1/data/afd9f936-bdc5-4811-9736-349a4b90933d/data/dna-sequences.fasta']' returned non-zero exit status 1.
Plugin error from alignment:
Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/var/folders/f6/744zv7hn72b8j94jxqfcs5rjrrwhlz/T/qiime2/toba1/data/afd9f936-bdc5-4811-9736-349a4b90933d/data/dna-sequences.fasta']' returned non-zero exit status 1.
See above for debug info.
real 213m15.456s
user 208m52.590s
sys 2m36.883s
Best,