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Question: error in running MiModD Variant Calling
1
gravatar for wdan213
9 months ago by
wdan213 • 10
wdan213 • 10 wrote:

I am a new user of MiModD (Previously, I use CloudMap to analysis WGS data from Hawaiian Variant Mapping method). I run MiModD on locally installed Galaxy interface. There is problem in running MiModD Variant Calling (version 0.1.8_1), it always shows me "tool error, Unable to finish job". I checked the information, it generated part of the data, but seems failed to finish the job. I tried with both the test data ( ot266 mutant strain data) and my personal data. Nothing wrong with the previous steps (MiModD Read Alignment, MiModD Run Annotation and MiModD Convert ). But the MiModD Variant Calling always reports this error. If anybody has the same issue?
software error • 338 views
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modified 9 months ago by Wolfgang Maier • 600 • written 9 months ago by wdan213 • 10
1
gravatar for Wolfgang Maier
9 months ago by
Wolfgang Maier • 600
Germany
Wolfgang Maier • 600 wrote:

Hi, the MiModD Variant Calling tool generates a BCF dataset, and Galaxy requires bcftools to index such files as part of finishing the job. Most likely, the error you are seeing is due to bcftools not being available to Galaxy. If you are getting this on an instance of Galaxy that you are administering you can simply install bcftools via the Admin Interface of Galaxy -> Manage Tool Dependencies -> check the dependencies under Set External Metadata -> click on Install checked dependencies using Conda. If you are not an Admin of your Galaxy instance, you will have to talk to the responsible person.
ADD COMMENT • link written 9 months ago by Wolfgang Maier • 600

Thank you very much, BCF tool installation makes the Variant Calling working!

ADD REPLY • link written 9 months ago by wdan213 • 10
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