Closed NagaComBio closed 2 years ago
Hi @NagaComBio
Sorry for the delay! I don't have a clear solution to this problem just from looking at the error message, but if you can share the data, e.g. with just a small slice of the bam, then I can try to reproduce the issue. If that's possible, you can email me at marianattestad@google.com.
For now I can tell you that --group_variants=false
is only applicable when using vcf_candidate_importer
, which is the most common way that this error occurs, since the input VCF for that can have multiple candidate variants in the same position, which isn't supposed to be possible when the candidates are generated by make_examples without vcf_candidate_importer
.
Thanks, Maria
Hi @MariaNattestad
Thanks for the offer, but it would be difficult to share the data without a DTA. So, I went back and reran the workflow (--num_shards=5
) for a short region around the above coordinates and then again for the complete chr1, both the tests ran through without any errors. And some of the candidate variants called earlier are not present here.
1 160351251 . T <*> 0 . END=160351253 GT:GQ:MIN_DP:PL 0/0:50:80:0,261,2609
1 160351254 . GTTTT G,<*> 9.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:9:79:18,33,0:0.417722,0:8,0,26,990,990,990
Not sure how it's resolved. But, I will close this issue for now and will reopen it if a similar error pops up during the rerun of all the chrs.
Thank you for looking into the issue, Naga
Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.3/docs/FAQ.md: Yes
Describe the issue: The error arises during the "postprocess_variants" step. The quick-test and a run on chr22 from the same sample ran through without any issue. I tried to use
group_variants=false
as suggested here. But a similar error/crash occurs at a different variant/location. A similar problem was reported here, but the final fix is not provided.Setup
Steps to reproduce:
I have also tried postprocessing with
group_variants
, which also produces a similar error.Does the quick start test work on your system? Please test with https://github.com/google/deepvariant/blob/r0.10/docs/deepvariant-quick-start.md. Is there any way to reproduce the issue by using the quick start? No, the quick start and also chr22 from the same sample ran through.
Any additional context: