Open snakesch opened 3 months ago
Can you provide the whole log as an attachment? It is really hard to debug with missing information.
How did you install the GATK Conda environment? Looks like a problem with the conda environment configuration. One possible reason could be that conda environment is not the version 4.3.0.0 is requesting.
I did not install the GATK conda environment. Instead, I created a singularity container using the GATK v4.3.0.0 docker image. Also, the GATK version I have outside container is v4.6.0.0, so the fact that GATK v4.3.0.0 got called means it was using the GATK came with the image.
We don't support singularity so I am not sure how to help if that's the version you are using.
Dear GATK developers,
Thank you very much for the tool! I recently encountered an issue while running GATK gCNV, specifically with the step GermlineCNVCaller in cohort mode. I ran the workflow using WDL and the GATK v4.3.0.0 docker image. I am not sure how the error should be interpreted and thus would like to seek your advice on debugging. Since the entire cohort contains 75 samples, I omitted some verbose debug messages in the error log below.
Much appreciated for your help indeed!
Best regards, Louis