MiModD Troubleshooting

usegalaxy.org support
1

Hi Wolfgang,

I also got a error recently when I used MiModD Variant Calling tool in public Galaxy server (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” }

2

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

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

Let’s start there :slight_smile:

3

Hi Jennifer,

Thanks for your kind reply. My history link is (Galaxy). 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.

Warm regards,

Wang Nie

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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

Thanks for the followup!

1 Like