Alignment error message

Hi @ebolyen

Thank you for your response. Actually, I have used denovo otu picking instead of closed one.

An off-topic reply has been split into a new topic: Q2-fragment-insertion runtime

Please keep replies on-topic in the future.

Hi, I’m experiencing the same issue. Here is the error message:

 qiime alignment mafft --i-sequences uchime-dn-out/rep-seqs-nonchimeric-dn.qza --p-n-threads 12 --output-dir alignment_out --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 12 /tmp/qiime2-archive-ufnc8jas/ed294b2b-71c6-4548-85f9-55aa95c4a6d8/data/dna-sequences.fasta

inputfile = orig
236215 x 534 - 35 d
nthread = 12
stacksize: 8192 kb->46135 kb
generating a scoring matrix for nucleotide (dist=200) ... done
Gap Penalty = -1.53, +0.00, +0.00

Making a distance matrix ..
/home/aescalante/miniconda3/envs/qiime2-18.2/bin/mafft: line 2440: 21139 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"
Plugin error from alignment:

  Command '['mafft', '--preservecase', '--inputorder', '--thread', '12', '/tmp/qiime2-archive-ufnc8jas/ed294b2b-71c6-4548-85f9-55aa95c4a6d8/data/dna-sequences.fasta']' returned non-zero exit status 1

Hi @abarron - sorry, we don’t have anything to report on this end — that error is coming from mafft, not from QIIME 2. I would suggest filing a bug report with the mafft team to see if they can provide some assistance. My best guess, at least according to earlier reports is that this is related to insufficient memory on the machine you are running this command on. With that said, it sounds like the memory requirements in some cases might be pretty crazy. It is possible that mafft isn’t behaving when you specify so many threads (the memory requirement might be increasing by a factor of 12, but I am not sure). I am sorry I don’t have a better answer for you, but if you want more assistance from us, do you think you could provide us with download links to your data, that way we can re-run the command you provided above? Thanks! :t_rex:

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