# Downstream jobs finishing first

**URL:** <https://help.galaxyproject.org/t/downstream-jobs-finishing-first/7463>\
**Category:** Uncategorized\
**Tags:** workflow, transcriptomics, stringtie\
**Created:** [February 4, 2022, 2:58pm UTC](https://help.galaxyproject.org/t/downstream-jobs-finishing-first/7463 "2022-02-04T14:58:58Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Kanishk](https://avatars.discourse-cdn.com/v4/letter/k/6de8d8/32.png) [@Kanishk](https://help.galaxyproject.org/u/Kanishk)\
**Post date:** [February 4, 2022, 2:58pm UTC](https://help.galaxyproject.org/t/downstream-jobs-finishing-first/7463/1 "2022-02-04T14:58:58Z")

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Hello,

I’m doing some basic de novo transcriptome analysis and have found that while I’m assembling transcripts in Stringtie, my downstream jobs such as running stringtiemerge, gffcompare, and featurecounts all finished even though I still had some original Stringtie jobs going…

And then DESeq2 fails to run. This doesn’t seem right, or even possible. Does anyone have any insight on this?

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**Author:** ![bjoern.gruening](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/bjoern.gruening/32/10_2.png) [@bjoern.gruening](https://help.galaxyproject.org/u/bjoern.gruening)\
**Post date:** [February 5, 2022, 9:22pm UTC](https://help.galaxyproject.org/t/downstream-jobs-finishing-first/7463/2 "2022-02-05T21:22:03Z")

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That should not happen, can you maybe share a history with us in which this happens?

I have never seen this before.

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**Author:** ![Kanishk](https://avatars.discourse-cdn.com/v4/letter/k/6de8d8/32.png) [@Kanishk](https://help.galaxyproject.org/u/Kanishk)\
**Post date:** [February 7, 2022, 6:57pm UTC](https://help.galaxyproject.org/t/downstream-jobs-finishing-first/7463/3 "2022-02-07T18:57:09Z")

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Unfortunately I ended up removing those datasets and starting over (I was running out of space). Since that attempt, I’ve just been running jobs in batch mode one at a time to avoid this issue. I will update this thread if this issue occurs again.

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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:** [February 8, 2022, 10:33pm UTC](https://help.galaxyproject.org/t/downstream-jobs-finishing-first/7463/4 "2022-02-08T22:33:55Z")

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Related Q&A [Stringtie not running](https://help.galaxyproject.org/t/stringtie-not-running/7487)

It seems that the problem was some setting in the workflow used.