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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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[bug report] CNNScoreVariants can't continue #8827

Open Ithinky opened 1 month ago

Ithinky commented 1 month ago

Bug Report

I run the CNNScoreVariants as tutorial, but it can't continue and always stuck as the following picture, and the programme isn't stop by any error. By the way I can't find gatkcondaenv.yml in anywhere. Can you upload it in the github, so that I can check
whether the bug is caused by loss of some python dependencies.

Affected tool(s) or class(es)

CNNScoreVariants

Affected version(s)

GATK4.3.0.0

Description

image

droazen commented 1 month ago

@Ithinky gatkcondaenv.yml is included in the zip file for each official release (https://github.com/broadinstitute/gatk/releases). It's also checked into the repository at: https://github.com/broadinstitute/gatk/blob/master/scripts/gatkcondaenv.yml.template

Please let us know if the issue persists when running within the standard Python environment.