# Bowtie2 error-bowtie2-align died with signal 6 (ABRT)

**URL:** <https://help.galaxyproject.org/t/bowtie2-error-bowtie2-align-died-with-signal-6-abrt/8795>\
**Category:** Uncategorized\
**Tags:** galaxy-local, mapping\
**Created:** [October 7, 2022, 10:56am UTC](https://help.galaxyproject.org/t/bowtie2-error-bowtie2-align-died-with-signal-6-abrt/8795 "2022-10-07T10:56:46Z")\
**Posts on this page:** 1\
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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [October 12, 2022, 10:00pm UTC](https://help.galaxyproject.org/t/bowtie2-error-bowtie2-align-died-with-signal-6-abrt/8795/3 "2022-10-12T22:00:19Z")

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Hi @Sayema and @gbbio

When I’ve seen this error, it was due to not having intact pairs present in the input fastq files.

That isn’t a requirement _always_ but ensuring intact pairs usually solves it. There is probably a specific option that is the trigger – but I don’t know for certain which 🙃

So, if filtering by length isn’t enough (minimum seed length), try this to get rid of reads in either read dataset that no longer have a mate present in the other read dataset. In short, ensure that intact pairs are input to the tool. Some QA tools sort the outputs by paired/not state but others will just remove reads from one end.

> [@Bowtie2 parameters for stringent alignment](https://help.galaxyproject.org/t/bowtie2-parameters-for-stringent-alignment/503/11):
>
> - `FastQ Interlacer` followed by `FastQ Deinterlacer`

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