# MimodD extract variant sites **URL:** \ **Category:** usegalaxy.org support\ **Tags:** mapping, server-open-issue\ **Created:** [July 6, 2023, 8:37am UTC](https://help.galaxyproject.org/t/mimodd-extract-variant-sites/10410 "2023-07-06T08:37:58Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![sen\_99](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sen_99/32/4492_2.png) [@sen\_99](https://help.galaxyproject.org/u/sen_99)\ **Post date:** [July 6, 2023, 8:37am UTC](https://help.galaxyproject.org/t/mimodd-extract-variant-sites/10410/1 "2023-07-06T08:37:58Z")
Hi everyone, I am trying to run MimodD extract variant sites tool with default settings in [Galaxy.org](http://Galaxy.org) and I got the below error for a week ago. I have used this tool many times and it has worked… Fatal error: Exit code 127 () /corral4/main/jobs/051/284/51284803/tool\_script.sh: line 10: mimodd: command not found I first aligned my fastq file using Map with BWA-MEM tool, then ran FilterBAM, MarkDuplicates, CleanSAM, Realign reads, MimodD Variant calling, and then tried to MimodD extract variant sites. I re-ran it several times, but got same error, tried to run this tool with the data that worked in the past, but got same error now. Could you help me? Thank you! Here is the bug report ### Detailed Job Information Job environment and execution information is available at the job [info page](https://usegalaxy.org/datasets/f9cad7b01a472135b38cb4f13b806d30/details). | Job ID | 51284803 (bbd44e69cb8906b5ca7ad95501fbcc85) | | --- | --- | | Tool ID | [toolshed.g2.bx.psu.edu/repos/wolma/mimodd\_main/mimodd\_varextract/0.1.9](http://toolshed.g2.bx.psu.edu/repos/wolma/mimodd_main/mimodd_varextract/0.1.9) | | Tool Version | 0.1.9 | | Job PID or DRM id | 42890615 | | Job Tool Version | /corral4/main/jobs/051/284/51284803/tool\_script.sh: line 9: mimodd: command not found | ### Job Execution and Failure Information #### Command Line mimodd varextract ‘/corral4/main/objects/3/a/b/dataset\_3ab6f1f4-e4f9-4f97-9ef1-f70de1dbe8c5.dat’ --ofile ‘/corral4/main/objects/6/0/6/dataset\_6069d9c4-28b2-40b3-868f-cba502a72c30.dat’ --verbose #### stderr /corral4/main/jobs/051/284/51284803/tool\_script.sh: line 10: mimodd: command not found #### stdout #### Job Information None #### Job Traceback None ---
**Author:** ![wm75](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/wm75/32/56_2.png) [@wm75](https://help.galaxyproject.org/u/wm75)\ **Post date:** [July 6, 2023, 6:55pm UTC](https://help.galaxyproject.org/t/mimodd-extract-variant-sites/10410/2 "2023-07-06T18:55:43Z")
@nate I’ve filed a bug report about this same problem. Can you take a look if you have time? @sen_99 there is nothing you’ve been doing wrong. It’s a problem with the tool installation on the server. Thanks for reporting! ---
**Author:** ![sen\_99](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sen_99/32/4492_2.png) [@sen\_99](https://help.galaxyproject.org/u/sen_99)\ **Post date:** [July 8, 2023, 2:31am UTC](https://help.galaxyproject.org/t/mimodd-extract-variant-sites/10410/3 "2023-07-08T02:31:15Z")
Thank you! I was relieved. As he says, I will try at EU for now. > [@MiModD Troubleshooting](https://help.galaxyproject.org/t/mimodd-troubleshooting/10393/4): > > 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! ---
**Author:** ![nate](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/nate/32/1752_2.png) [@nate](https://help.galaxyproject.org/u/nate)\ **Post date:** [July 21, 2023, 10:48pm UTC](https://help.galaxyproject.org/t/mimodd-extract-variant-sites/10410/4 "2023-07-21T22:48:56Z")
This should now be working at [usegalaxy.org](http://usegalaxy.org) again. Sorry for the trouble, and please let us know if you continue to encounter issues. ---
**Author:** ![sen\_99](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/sen_99/32/4492_2.png) [@sen\_99](https://help.galaxyproject.org/u/sen_99)\ **Post date:** [July 26, 2023, 10:53am UTC](https://help.galaxyproject.org/t/mimodd-extract-variant-sites/10410/5 "2023-07-26T10:53:18Z")
@nate Thank you! I confirmed it works now! ---
**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:** [September 11, 2023, 5:45pm UTC](https://help.galaxyproject.org/t/mimodd-extract-variant-sites/10410/6 "2023-09-11T17:45:44Z")
Split this topic on September 11, 2023, 5:45pm UTC A post was split to a new topic: [Troubleshooting MiModD](https://help.galaxyproject.org/t/troubleshooting-mimodd/10771)