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google / deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
BSD 3-Clause "New" or "Revised" License
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DeepSomatic freezes after call_variants when there is 0 example #8

Closed proteinosome closed 3 months ago

proteinosome commented 8 months ago

@kishwarshafin Khi PIn here. Filing a report of an issue I'm seeing. I'm trying to implement DeepSomatic into a pipeline. What the pipeline does now is that it splits the genome into equal interval and uses the --region parameter to call variants in just that region. However, when I was testing this with a toy example which doesn't have variants in most intervals, the DeepSomatic step stops progressing after call_variants.

Attaching a zip file of the log files collected here with the command used (command file). Thanks.

logs.zip

kishwarshafin commented 8 months ago

Hi @proteinosome , Thank you very much for reporting this. I can confirm this is reproducible. I will work on a fix soon.

kishwarshafin commented 3 months ago

hi @proteinosome , we are currently fixing this issue. We will push a fix very soon.

kishwarshafin commented 3 months ago

This issue should be fixed in 1.6.1, please feel free to reopen if you that's not the case.