Mafft error with virtual box

Hello. I have successfully installed Qiime2-2018.4 on my virtual box running Ubuntu. When attempting to run alignment mafft with the verbose setting, I get the following output.

qiime alignment mafft --verbose --i-
sequences rep-seqs16S.qza --o-alignment aligned-rep-seqs16S.qza
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-f7w26wyx/62e87efe-51a9-454e-8935-82e5168eb19c/data/dna-sequences.fasta

inputfile = orig
836222 x 445 - 267 d
nthread = 1
stacksize: 8192 kb->163324 kb
generating a scoring matrix for nucleotide (dist=200) … done
Gap Penalty = -1.53, +0.00, +0.00

Making a distance matrix …
/home/qiime2/miniconda/envs/qiime2-2018.4/bin/mafft: line 2440: 2982 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/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/”, line 274, in call
results = action(**arguments)
File “”, line 2, in mafft
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/”, line 231, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/”, line 366, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_alignment/”, line 61, in mafft
run_command(cmd, aligned_fp)
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_alignment/”, line 27, in run_command, stdout=output_f, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘/tmp/qiime2-archive-f7w26wyx/62e87efe-51a9-454e-8935-82e5168eb19c/data/dna-sequences.fasta’]’ returned non-zero exit status 1

Plugin error from alignment:

Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’, ‘/tmp/qiime2-archive-f7w26wyx/62e87efe-51a9-454e-8935-82e5168eb19c/data/dna-sequences.fasta’]’ returned non-zero exit status 1

See above for debug info.

Where do i go from here?

Hi there @mshelomi1!

This looks like MAFFT ran out of memory while working. You could try to increase the memory available on your virtual machine, check out these posts for more:

Let us know how it goes. :t_rex: :qiime2:

It’s already at maximum, around 35GB RAM. The file is just too big. Thanks anyway.

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