# Alignment error message

**URL:** https://forum.qiime2.org/t/alignment-error-message/2383
**Category:** User Support
**Tags:** mafft
**Created:** [January 2, 2018, 5:38pm UTC](https://forum.qiime2.org/t/alignment-error-message/2383 "2018-01-02T17:38:47Z")
**Posts on this page:** 1
**Showing post:** 36

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### Author: ![abarron](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/a/ebca7d/32.png) [@abarron](https://forum.qiime2.org/u/abarron)
#### Post date: [April 10, 2018, 1:49pm UTC](https://forum.qiime2.org/t/alignment-error-message/2383/36 "2018-04-10T13:49:41Z")

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

```auto
 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
```

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