# bowtie2 not working

**URL:** <https://help.galaxyproject.org/t/bowtie2-not-working/2142>\
**Category:** usegalaxy.org support\
**Tags:** troubleshooting, mapping\
**Created:** [September 19, 2019, 9:08pm UTC](https://help.galaxyproject.org/t/bowtie2-not-working/2142 "2019-09-19T21:08:11Z")\
**Posts on this page:** 1\
**Showing post:** 26

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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 10, 2019, 5:03pm UTC](https://help.galaxyproject.org/t/bowtie2-not-working/2142/26 "2019-10-10T17:03:18Z")

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**Update:** Fixed

@nibhelim @Jamal_Williams @Athina @Priscilla607 and any others that ran into this issue, with any mapping tool over the last few weeks

> [@Tophat not working??? - Deprecated tool, use HISAT2 instead](https://help.galaxyproject.org/t/tophat-not-working-deprecated-tool-use-hisat2-instead/2256/3):
>
> _Note to all end users running mapping:_ Using all defaults for the “Job Resources” parameter is a good choice now again. No need to target a particular cluster anymore. Allowing Galaxy to choose the target cluster based on the currently available resources, at the time of job submission, is the fastest way to run tools.
> 
> Ticket: [Mapping jobs failing on Jetstream cluster · Issue #257 · galaxyproject/usegalaxy-playbook · GitHub](https://github.com/galaxyproject/usegalaxy-playbook/issues/257#issuecomment-540676708)

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