# MiModD Troubleshooting

**URL:** <https://help.galaxyproject.org/t/mimodd-troubleshooting/10393>\
**Category:** usegalaxy.org support\
**Tags:** troubleshooting\
**Created:** [July 2, 2023, 1:50pm UTC](https://help.galaxyproject.org/t/mimodd-troubleshooting/10393 "2023-07-02T13:50:11Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![WangNIE](https://avatars.discourse-cdn.com/v4/letter/w/2bfe46/32.png) [@WangNIE](https://help.galaxyproject.org/u/WangNIE)\
**Post date:** [July 2, 2023, 1:50pm UTC](https://help.galaxyproject.org/t/mimodd-troubleshooting/10393/1 "2023-07-02T13:50:11Z")

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Hi Wolfgang,

I also got a error recently when I used MiModD Variant Calling tool in public Galaxy server ([https://usegalaxy.org/](https://usegalaxy.org/)) after aligned with Bowtie2.

I tried to repeat this step (by ‘Run Job Again’) in a previous successful analysis case and got the same error. Could you give me any suggestions?

Thanks.

Error code:

/corral4/main/jobs/051/303/51303573/tool\_script.sh: line 10: mimodd: command not found.

Job Information

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/wolma/mimodd\_main/mimodd\_varcall/0.1.9

Command Line empty

Tool Standard Output empty

Tool Standard Error

/corral4/main/jobs/051/303/51303573/tool\_script.sh: line 10: mimodd: command not found

Tool Exit Code: 127

Job Messages

{ “code\_desc”: “”, “desc”: “Fatal error: Exit code 127 ()”, “error\_level”: 3, “exit\_code”: 127, “type”: “exit\_code” }

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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:** [July 3, 2023, 7:43pm UTC](https://help.galaxyproject.org/t/mimodd-troubleshooting/10393/2 "2023-07-03T19:43:29Z")

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Hi @WangNIE

Thanks for posting back the logs. The message “mimodd: command not found” could be a cluster configuration issue OR some input issue the tool doesn’t understand how to handle.

Examples: an empty or header-only BAM could be a trigger. A mismatched reference genome or poor alignment rates would _probably_ produce something more informative. If that BAM was from Upload and not a job run in Galaxy, or from using a custom reference genome+build, more could be going on data-wise leading to the error.

Would you please generate and share back a link to the history? [Troubleshooting errors](https://training.galaxyproject.org/training-material/faqs/galaxy/analysis_troubleshooting.html)

If you are following a tutorial, or using tutorial data, please also link that back for context.

Let’s start there 🙂

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**Author:** ![WangNIE](https://avatars.discourse-cdn.com/v4/letter/w/2bfe46/32.png) [@WangNIE](https://help.galaxyproject.org/u/WangNIE)\
**Post date:** [July 4, 2023, 3:20am UTC](https://help.galaxyproject.org/t/mimodd-troubleshooting/10393/3 "2023-07-04T03:20:35Z")

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Hi Jennifer,

Thanks for your kind reply. My history link is ([Galaxy](https://usegalaxy.org/u/sht_wangnie/h/yan357)). And I submited a bug report just now. Actually I tried re-running the MiModD Variant Calling (by ‘Run Job Again’) in a previous successful analysis history but got the same error (command not found).

Wolfgang said this maybe an issue with MiModD installation in [usegalaxy.org](http://usegalaxy.org).

Warm regards,

Wang Nie

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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:** [July 6, 2023, 10:41pm UTC](https://help.galaxyproject.org/t/mimodd-troubleshooting/10393/4 "2023-07-06T22:41:24Z")

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Hi @WangNIE

We have confirmed the problem at the US server. Please try at EU or AU for now.

Consolidating this this post, where we will post updates: [MimodD extract variant sites](https://help.galaxyproject.org/t/mimodd-extract-variant-sites/10410)

Thanks for the followup!

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<div class="post-metadata">

**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:** [July 6, 2023, 10:41pm UTC](https://help.galaxyproject.org/t/mimodd-troubleshooting/10393/5 "2023-07-06T22:41:31Z")

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Closed on July 6, 2023, 10:41pm UTC