Not all shards generated about deepvariant HOT 5 CLOSED

@ErinKinghorn somewhat confusingly, shard specifies are 0-based for the first number (shard index) and 1-indexed for the second (count).

So your first shard is 00000-of-00032 and your last shard is 00031-of-00032. Can you confirm that you indeed are observing only 31 output files?

The message you report here looks normal - and the warning should not make a difference.

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@ErinKinghorn ,

Once you follow @danielecook 's suggestion to see if the files look good. If you in fact find the files look normal, can you please test this docker:

docker pull google/deepvariant:CL602468145
docker pull google/deepvariant:CL602468145-gpu

It seems like this issue is related to a this issue: #769

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Thank you for the feedback! @danielecook I can confirm that the files in the tmp directory do look to be normal as you described above. @kishwarshafin, I tested the docker that you suggested and now it seems that Deepvariant did not run at all (vcfs and gvcfs are empty)
deepvarrun_b37_MND_G33.1kei.log

I have attached a log file for one of the samples, so you can see what happened.

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I have picked up an error in the original cram files for the 4 samples that did not work. Thank you for the help!

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Hi @ErinKinghorn , if I understand your latest comment, you meant that you were able to get them to work now?
If so, I'll close this. (But if I misunderstood, please reopen with more questions!)

@kishwarshafin will plan to do a 1.6.1 release to fix the issue above (and will officially publish a Docker). Thanks for helping us test!

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