Merging vcf files error with glnexus:v1.2.7 about deepvariant HOT 6 CLOSED

Looks like this is the GLnexus question. Could you please post the question at GLNexus page
Also, from the log output it looks like GLnexus was completed successfully.

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Hi @poddarharsh15

Actually, can you go back in your log and confirm that DeepTrio runs actually finish correctly?

If I remember correctly, our run_deeptrio one-step script might continue to run the following steps even when previous steps failed.

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And, follow up on @akolesnikov 's point, if you have gotten to this point, it would seem like these files should be complete?

/output/HG002.g.vcf.gz \
/output/HG003.g.vcf.gz \
/output/HG004.g.vcf.gz \

If you can examine those files and confirm, that will be great. (Or look at the log like I mentioned before. But given you have the files, checking the files directly might be easier :))

from deepvariant.

Hi @pichuan, @akolesnikov,

I'm new to DeepTrio and couldn't locate the log files, but I have intermediate results showing that DeepTrio ran successfully without errors. Additionally, I successfully benchmarked the .vcf files generated by DeepTrio. I've attached screenshots for reference. Your assistance is greatly appreciated.
Thank you

finished log

Benchmark

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Hi @poddarharsh15 , it seems like you're certain that the DeepTrio run finished correctly.
In that case, I agree with @akolesnikov 's original assessment that this can be an issue for the downstream glnexus step, which we can't directly support.

One suggestion to try:
If you need to check your run a bit more closely, maybe breaking it down to just running this part first:

udocker run \
-v "${PWD}/output":"/output" \
quay.io/mlin/glnexus:v1.2.7 \
/usr/local/bin/glnexus_cli \
--config DeepVariant_unfiltered \
/output/HG002.g.vcf.gz \
/output/HG003.g.vcf.gz \
/output/HG004.g.vcf.gz

before piping to the next step. Maybe that could help you identify what the errors are coming out from that step?

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Closing the issue. Feel free to reopen as needed.

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