Not a BGZF file about octopus HOT 5 CLOSED

Is that 6 minutes to variant call a human ??

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Hi Jared,

Thanks for reporting this. Although I can't reproduce the issue on my machine, I think I know what's going on. Basically octopus will try to generate an index for compressed VCF (or BCF) output. This happens on destruction of the handle to the file. When the handle gets moved around early in the run (before anything has been written) the 'moved from' handle gets destroyed. I think the old handle remains in a valid state in your setup and therefore attempts to build an index on the empty file, which triggers this warning.

This shouldn't have any adverse affects downstream, but I've added some additional checks to stop the index being generated on empty handles. Would you mind checking out the develop branch and seeing if the warning is still being generated?

Many thanks,
Dan

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Is that 6 minutes to variant call a human ??

@iqbal-lab Alas no, this is on a ~100MB test .bam. Still, we are seeing running times of ~75mins with --fast enabled on WGS 30x data on a 20-core node

@dancooke checking develop now

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Wow.

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@dancooke

I can confirm that I no longer see the warning message in the develop branch. Thanks for the fast response.

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