# Fatal error: exit code 1 () using cuffdiff

**URL:** <https://help.galaxyproject.org/t/fatal-error-exit-code-1-using-cuffdiff/467>\
**Category:** Uncategorized\
**Tags:** deprecated\
**Created:** [January 17, 2019, 7:03pm UTC](https://help.galaxyproject.org/t/fatal-error-exit-code-1-using-cuffdiff/467 "2019-01-17T19:03:32Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![jessd](https://avatars.discourse-cdn.com/v4/letter/j/ce73a5/32.png) [@jessd](https://help.galaxyproject.org/u/jessd)\
**Post date:** [January 17, 2019, 7:03pm UTC](https://help.galaxyproject.org/t/fatal-error-exit-code-1-using-cuffdiff/467/1 "2019-01-17T19:03:32Z")

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I am trying to analyze RNA data samples and I have gotten through the pipeline (through cuffdiff) once before however I forgot to generate an SQLITE file so that I could visualize the data in CummeRbund. Now when I try to rerun CuffDiff and generate the SQLITE file I feel receiving an error of exit code 1 ().

How can I fix this?

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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:** [January 17, 2019, 8:00pm UTC](https://help.galaxyproject.org/t/fatal-error-exit-code-1-using-cuffdiff/467/2 "2019-01-17T20:00:25Z")

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Hi, The Cuffdiff SQLite output options were problematic for a long time with the latest tool wrapper and we decided not to fix the problem last year ([ticket with details](https://github.com/galaxyproject/usegalaxy-playbook/issues/50)). Instead, the tool was deprecated at both the Galaxy Main [https://usegalaxy.org](https://usegalaxy.org) and Galaxy EU [https://usegalaxy.eu](https://usegalaxy.eu) public servers. Some people have luck with earlier versions (if available at public sites) and in their own Galaxy installs. You can try using it other places, or earlier versions, but please know that the Galaxy wrapped versions of the tools (all Cuff\* tools) are no longer actively being supported/developed further at this time, and that will likely stay true going forward.

We recommended using more current/updated tools and methods for RNA-seq differential expression analysis. Please see the Galaxy tutorials for example protocols:

> [@Troubleshooting resources for errors or unexpected results](https://help.galaxyproject.org/t/troubleshooting-resources-for-errors-or-unexpected-results/42/1):
>
> [Galaxy Training Network Tutorials](https://galaxyproject.github.io/training-material/): Some [GTN](https://galaxyproject.org/teach/gtn/) tutorials are appropriate for [Galaxy Main](https://usegalaxy.org) and some are not. Where you can run each is noted per tutorial – click on the _Galaxy instances_ gear icon ![galaxyserversGTN](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/1X/1287f50cfcdaa1aad750fe323f96995260ac4947.png) to review the [Public Galaxy](https://galaxyproject.org/use/) server choices. If a tutorial is supported by a pre-configured [Galaxy Docker](https://hub.docker.com/r/bgruening/galaxy-stable/) training image, instructions for how to get it will be listed below the tutorial listings, per category.