Can genotypegvcf input multi-sample g.vcf files?

Healthcare & Life Sciences Parabricks
1

I tried 400-sample gvcf to Parabriks genotypegvcf and can complete successfully, while I input 800±sample gvcf, the log shows something wrong
like this:

[PB Info 2024-Apr-28 09:16:32] ------------------------------------------------------------------------------
[PB Info 2024-Apr-28 09:16:32] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Apr-28 09:16:32] || Version 4.0.0-1 ||
[PB Info 2024-Apr-28 09:16:32] || genotypegvcf ||
[PB Info 2024-Apr-28 09:16:32] ------------------------------------------------------------------------------
[PB Info 2024-Apr-28 09:16:32] ProgressMeter - Current-Locus Elapsed-Minutes
[PB Info 2024-Apr-28 09:16:33] ProgressMeter - :0 0.0
[PB Info 2024-Apr-28 09:16:34] ProgressMeter - :0 0.0
[PB Info 2024-Apr-28 09:16:35] ProgressMeter - :0 0.1
[PB Info 2024-Apr-28 09:16:36] ProgressMeter - :0 0.1
[PB Info 2024-Apr-28 09:16:37] ProgressMeter - :0 0.1
[PB Info 2024-Apr-28 09:16:38] ProgressMeter - :0 0.1
[PB Info 2024-Apr-28 09:16:39] ProgressMeter - :0 0.1
[PB Info 2024-Apr-28 09:16:40] ProgressMeter - :0 0.1
[PB Info 2024-Apr-28 09:16:41] ProgressMeter - :0 0.2
[PB Info 2024-Apr-28 09:16:42] ProgressMeter - :0 0.2
[PB Info 2024-Apr-28 09:16:43] ProgressMeter - :0 0.2
[PB Info 2024-Apr-28 09:16:44] ProgressMeter - :0 0.2
[PB Info 2024-Apr-28 09:16:45] ProgressMeter - :0 0.2
[PB Info 2024-Apr-28 09:16:46] ProgressMeter - :0 0.2
[PB Info 2024-Apr-28 09:16:47] ProgressMeter - :0 0.2
[PB Info 2024-Apr-28 09:16:48] ProgressMeter - :0 0.3
[PB Info 2024-Apr-28 09:16:49] ProgressMeter - :0 0.3
[PB Info 2024-Apr-28 09:16:50] ProgressMeter - :0 0.3
[PB Info 2024-Apr-28 09:16:51] ProgressMeter - :0 0.3
[PB Info 2024-Apr-28 09:16:52] ProgressMeter - :0 0.3
[PB Info 2024-Apr-28 09:16:53] ProgressMeter - :0 0.3
[PB Info 2024-Apr-28 09:16:54] ProgressMeter - :0 0.4
[PB Info 2024-Apr-28 09:16:55] ProgressMeter - :0 0.4
[PB Info 2024-Apr-28 09:16:56] ProgressMeter - :0 0.4
[PB Info 2024-Apr-28 09:16:57] ProgressMeter - :0 0.4
[PB Info 2024-Apr-28 09:16:58] ProgressMeter - :0 0.4
[PB Info 2024-Apr-28 09:16:59] ProgressMeter - :0 0.4
[PB Info 2024-Apr-28 09:17:01] ProgressMeter - :0 0.5
[PB Info 2024-Apr-28 09:17:02] ProgressMeter - :0 0.5
[PB Info 2024-Apr-28 09:17:03] ProgressMeter - :0 0.5
[PB Info 2024-Apr-28 09:17:04] ProgressMeter - :0 0.5
[PB Info 2024-Apr-28 09:17:05] ProgressMeter - :0 0.5
[PB Info 2024-Apr-28 09:17:06] ProgressMeter - :0 0.6
[PB Info 2024-Apr-28 09:17:07] ProgressMeter - :0 0.6
[PB Info 2024-Apr-28 09:17:08] ProgressMeter - :0 0.6
[PB Info 2024-Apr-28 09:17:09] ProgressMeter - :0 0.6
[PB Info 2024-Apr-28 09:17:10] ProgressMeter - :0 0.6
[PB Info 2024-Apr-28 09:17:11] ProgressMeter - :0 0.6
[PB Info 2024-Apr-28 09:17:12] ProgressMeter - :0 0.6
[PB Info 2024-Apr-28 09:17:13] ProgressMeter - :0 0.7
[PB Info 2024-Apr-28 09:17:14] ProgressMeter - :0 0.7
[PB Info 2024-Apr-28 09:17:15] ProgressMeter - :0 0.7
[PB Info 2024-Apr-28 09:17:16] ProgressMeter - :0 0.7
[PB Info 2024-Apr-28 09:17:17] ProgressMeter - :0 0.7
[PB Info 2024-Apr-28 09:17:18] ProgressMeter - :0 0.8
[PB Info 2024-Apr-28 09:17:19] ProgressMeter - :0 0.8
[PB Info 2024-Apr-28 09:17:20] ProgressMeter - :0 0.8
[PB Info 2024-Apr-28 09:17:21] ProgressMeter - :0 0.8
[PB Info 2024-Apr-28 09:17:22] ProgressMeter - :0 0.8
[PB Info 2024-Apr-28 09:17:23] ProgressMeter - :0 0.8
[PB Info 2024-Apr-28 09:17:24] ProgressMeter - :0 0.9
[PB Info 2024-Apr-28 09:17:25] ProgressMeter - :0 0.9
[PB Info 2024-Apr-28 09:17:26] ProgressMeter - :0 0.9
[PB Info 2024-Apr-28 09:17:27] ProgressMeter - :0 0.9
[PB Info 2024-Apr-28 09:17:28] ProgressMeter - :0 0.9
[PB Info 2024-Apr-28 09:17:29] ProgressMeter - :0 0.9
[PB Info 2024-Apr-28 09:17:30] ProgressMeter - :0 0.9
[PB Info 2024-Apr-28 09:17:31] ProgressMeter - :0 1.0
[PB Info 2024-Apr-28 09:17:32] ProgressMeter - :0 1.0
[PB Info 2024-Apr-28 09:17:33] ProgressMeter - :0 1.0
[PB Info 2024-Apr-28 09:17:34] ProgressMeter - :0 1.0

while the normal log is:

[PB Info 2024-Apr-28 08:54:49] ------------------------------------------------------------------------------
[PB Info 2024-Apr-28 08:54:49] || Parabricks accelerated Genomics Pipeline ||
[PB Info 2024-Apr-28 08:54:49] || Version 4.0.0-1 ||
[PB Info 2024-Apr-28 08:54:49] || genotypegvcf ||
[PB Info 2024-Apr-28 08:54:49] ------------------------------------------------------------------------------
[PB Info 2024-Apr-28 08:54:49] ProgressMeter - Current-Locus Elapsed-Minutes
[PB Info 2024-Apr-28 08:54:50] ProgressMeter - chr01:41569395 0.0
[PB Info 2024-Apr-28 08:54:51] ProgressMeter - chr01:41592089 0.0
[PB Info 2024-Apr-28 08:54:52] ProgressMeter - chr01:41622155 0.1
[PB Info 2024-Apr-28 08:54:53] ProgressMeter - chr01:41660561 0.1
[PB Info 2024-Apr-28 08:54:54] ProgressMeter - chr01:41667652 0.1
[PB Info 2024-Apr-28 08:54:55] ProgressMeter - chr01:41707635 0.1
[PB Info 2024-Apr-28 08:54:56] ProgressMeter - chr01:41735027 0.1
[PB Info 2024-Apr-28 08:54:57] ProgressMeter - chr01:41764653 0.1
[PB Info 2024-Apr-28 08:54:58] ProgressMeter - chr01:41794196 0.2
[PB Info 2024-Apr-28 08:54:59] ProgressMeter - chr01:41831544 0.2
[PB Info 2024-Apr-28 08:55:00] ProgressMeter - chr01:41853510 0.2
[PB Info 2024-Apr-28 08:55:01] ProgressMeter - chr01:41891748 0.2
[PB Info 2024-Apr-28 08:55:02] ProgressMeter - chr01:41926134 0.2
[PB Info 2024-Apr-28 08:55:03] ProgressMeter - chr01:41960563 0.2
[PB Info 2024-Apr-28 08:55:04] ProgressMeter - chr01:41984755 0.2
[PB Info 2024-Apr-28 08:55:05] ProgressMeter - chr01:42013801 0.3
[PB Info 2024-Apr-28 08:55:06] ProgressMeter - chr01:42042525 0.3
[PB Info 2024-Apr-28 08:55:07] ProgressMeter - chr01:42070425 0.3
[PB Info 2024-Apr-28 08:55:08] ProgressMeter - chr01:42099326 0.3
[PB Info 2024-Apr-28 08:55:09] ProgressMeter - chr01:42116650 0.3
[PB Info 2024-Apr-28 08:55:10] ProgressMeter - chr01:42148216 0.3
[PB Info 2024-Apr-28 08:55:11] ProgressMeter - chr01:42186927 0.4
[PB Info 2024-Apr-28 08:55:12] ProgressMeter - chr01:42223098 0.4
[PB Info 2024-Apr-28 08:55:13] ProgressMeter - chr01:42282570 0.4
[PB Info 2024-Apr-28 08:55:14] ProgressMeter - chr01:42310950 0.4
[PB Info 2024-Apr-28 08:55:15] ProgressMeter - chr01:42354918 0.4
[PB Info 2024-Apr-28 08:55:16] ProgressMeter - chr01:42372708 0.4
[PB Info 2024-Apr-28 08:55:17] ProgressMeter - chr01:42402693 0.5
[PB Info 2024-Apr-28 08:55:18] genotypeGVCF finished, total time is 29.008 seconds
[PB Info 2024-Apr-28 08:55:18] ------------------------------------------------------------------------------
[PB Info 2024-Apr-28 08:55:18] || Program: genotypegvcf ||
[PB Info 2024-Apr-28 08:55:18] || Version: 4.0.0-1 ||
[PB Info 2024-Apr-28 08:55:18] || Start Time: Sun Apr 28 08:54:49 2024 ||
[PB Info 2024-Apr-28 08:55:18] || End Time: Sun Apr 28 08:55:18 2024 ||
[PB Info 2024-Apr-28 08:55:18] || Total Time: 29 seconds ||
[PB Info 2024-Apr-28 08:55:18] ------------------------------------------------------------------------------
real 0m29.180s
user 2m29.578s
sys 0m1.432s

So, I want to know if there are limits when input multi-sample g.vcf to Parabricks genotypegvcf
and my Parabricks version is 4.0.0-1 , GPU is A30

2

Have you resolved it now? I’m also curious about methods for combining multiple GVCF files. Currently, I’m using the GenomicDB workflow in GATK. I know that Parabricks’ genotypegvcf can only convert a single sample from GVCF to VCF. I’m also interested in learning how to merge multiple samples simultaneously to generate a final VCF file.

3

I have successfully tested genotyping gVCF with Parabricks on 400 samples, but more samples have not been successful.

4

The gVCF you input for genotype contained more than 1 sample, right?
How did you get the combined gVCF?

5

GATK CombineGVCFs