# Re: Alignment error message
**URL:** https://forum.qiime2.org/t/re-alignment-error-message/19002
**Category:** Technical Support
**Tags:** mafft
**Created:** [March 27, 2021, 4:43am UTC](https://forum.qiime2.org/t/re-alignment-error-message/19002 "2021-03-27T04:43:54Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@Willm\_Martens-Habben](https://forum.qiime2.org/u/Willm_Martens-Habben)
#### Post date: [March 27, 2021, 4:43am UTC](https://forum.qiime2.org/t/re-alignment-error-message/19002/1 "2021-03-27T04:43:54Z")
this might be a little outdated, but just for the record:
In response to @coralgal's post regarding an error message when running
qiime alignment mafft --i-sequences rep-seqs.qza --o-alignment aligned-rep-seqs.qza in earlier qiime2 builds.
> [@Alignment error message](https://forum.qiime2.org/t/alignment-error-message/2383):
>
> Hi there, I have been trying to align my sequences by running the maaft command. It crops up with this error. (qiime2-2017.11) qiime2@qiime2core2017-11:~/gbstrial2$ qiime alignment mafft \ \> --i-sequences rep-seqs.qza \ \> --o-alignment aligned-rep-seqs.qza Plugin error from alignment: Command '['mafft', '--preservecase', '--inputorder', '--thread', '1', '/tmp/qiime2-archive-zibb0xaz/25fd7c9d-1d26-460b-82e0-b9b3b148d570/data/dna-sequences.fasta']' returned non-zero exit status 1 Debug i…
I came across this same issue/error message while using qiime2-2020.2.
It was solved when I modified the command using the --p-n-threads auto flag:
qiime alignment mafft --i-sequences rep-seqs.qza --o-alignment aligned-rep-seqs.qza --p-n-threads auto
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### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [April 27, 2021, 10:44am UTC](https://forum.qiime2.org/t/re-alignment-error-message/19002/2 "2021-04-27T10:44:26Z")
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