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/commands.py", 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/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", 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/_mafft.py", line 61, in mafft
run_command(cmd, aligned_fp)
File "/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_alignment/_mafft.py", line 27, in run_command
subprocess.run(cmd, stdout=output_f, check=True)
File "/home/qiime2/miniconda/envs/qiime2-2018.4/lib/python3.5/subprocess.py", 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?
Thanks

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:

https://forum.qiime2.org/search?q=virtualbox%20memory

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.

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.