# HISAT2 Problems on Galaxy

**URL:** <https://help.galaxyproject.org/t/hisat2-problems-on-galaxy/1730>\
**Category:** usegalaxy.org support\
**Tags:** upload\
**Created:** [July 12, 2019, 7:04pm UTC](https://help.galaxyproject.org/t/hisat2-problems-on-galaxy/1730 "2019-07-12T19:04:03Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![Joe\_Hoolachan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/joe_hoolachan/32/301_2.png) [@Joe\_Hoolachan](https://help.galaxyproject.org/u/Joe_Hoolachan)\
**Post date:** [July 12, 2019, 7:04pm UTC](https://help.galaxyproject.org/t/hisat2-problems-on-galaxy/1730/1 "2019-07-12T19:04:03Z")

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I’ve tried uploading some fastqsanger files onto HISAT2. I have done this operation many times previously with the same data and it was able to work effectively. However, this time the operation has failed and this warning note came up:

Remote job server indicated a problem running or monitoring this job.

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**Author:** ![marten](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/marten/32/6_2.png) [@marten](https://help.galaxyproject.org/u/marten)\
**Post date:** [July 12, 2019, 7:07pm UTC](https://help.galaxyproject.org/t/hisat2-problems-on-galaxy/1730/2 "2019-07-12T19:07:38Z")

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Did this happen when you were uploading data, or when you were executing hisat2 tool?

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**Author:** ![Joe\_Hoolachan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/joe_hoolachan/32/301_2.png) [@Joe\_Hoolachan](https://help.galaxyproject.org/u/Joe_Hoolachan)\
**Post date:** [July 12, 2019, 7:14pm UTC](https://help.galaxyproject.org/t/hisat2-problems-on-galaxy/1730/3 "2019-07-12T19:14:50Z")

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Executing the HISAT2 tool.

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**Author:** ![RichardBJ](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/richardbj/32/560_2.png) [@RichardBJ](https://help.galaxyproject.org/u/RichardBJ)\
**Post date:** [July 14, 2019, 8:53am UTC](https://help.galaxyproject.org/t/hisat2-problems-on-galaxy/1730/4 "2019-07-14T08:53:16Z")

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You’ve tried re-uploading obviously haven’t you? I have known mysterious corruption occurring to a fastsanger between downloading to my workstation and uploading to my Galaxy server (ie first clue was strange HiSAT2 behaviour). Never pinned down where that happened, but redoing the whole process fixed it?

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**Author:** ![Camille\_Brewer](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/camille_brewer/32/785_2.png) [@Camille\_Brewer](https://help.galaxyproject.org/u/Camille_Brewer)\
**Post date:** [July 18, 2019, 5:46pm UTC](https://help.galaxyproject.org/t/hisat2-problems-on-galaxy/1730/6 "2019-07-18T17:46:02Z")

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I had the same exact error! Did you ever fix it?

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**Author:** ![Joe\_Hoolachan](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/joe_hoolachan/32/301_2.png) [@Joe\_Hoolachan](https://help.galaxyproject.org/u/Joe_Hoolachan)\
**Post date:** [July 18, 2019, 5:57pm UTC](https://help.galaxyproject.org/t/hisat2-problems-on-galaxy/1730/7 "2019-07-18T17:57:57Z")

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Hi, I ended up deleting the data and reuploaded it. It seemed to work fine there.