# Mafft error for alignment of rep-seqs

**URL:** https://forum.qiime2.org/t/mafft-error-for-alignment-of-rep-seqs/3915
**Category:** User Support
**Tags:** mafft
**Created:** [April 25, 2018, 7:00am UTC](https://forum.qiime2.org/t/mafft-error-for-alignment-of-rep-seqs/3915 "2018-04-25T07:00:20Z")
**Posts on this page:** 1
**Showing post:** 8

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### Author: ![gilberto\_solano](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/g/ecc23a/32.png) [@gilberto\_solano](https://forum.qiime2.org/u/gilberto_solano)
#### Post date: [April 29, 2018, 2:28pm UTC](https://forum.qiime2.org/t/mafft-error-for-alignment-of-rep-seqs/3915/8 "2018-04-29T14:28:15Z")

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It looks like this is an old trouble, maybe related to memory or an internal process in mafft, as observed here:

> [@Alignment error message](https://forum.qiime2.org/t/alignment-error-message/2383/36):
>
> 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-ufn…

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