Pbrun haplotypecaller running error

Healthcare & Life Sciences Parabricks
1

When I use haplotypecaller for calling, the following error is prompted. I would like to know where the cause of this error comes from. Thanks

[PB Info 2024-Dec-12 19:10:22] C49844049:1      67.2    10328918        153780
[PB Info 2024-Dec-12 19:10:32] C49930808:1      67.3    10352344        153747
[PB Info 2024-Dec-12 19:10:42] C50013076:1      67.5    10373677        153684
[PB Info 2024-Dec-12 19:10:52] C50092022:1      67.7    10396342        153640
[PB Info 2024-Dec-12 19:11:02] C50163555:1      67.8    10417550        153575
[PB Info 2024-Dec-12 19:11:12] C50260359:1      68.0    10444108        153589
[PB Info 2024-Dec-12 19:11:22] C50348742:1      68.2    10469902        153592
[PB Info 2024-Dec-12 19:11:32] C50445650:1      68.3    10498570        153637
[PB Info 2024-Dec-12 19:11:42] C50524100:1      68.5    10521775        153602
[PB Info 2024-Dec-12 19:11:52] C50680740:1      68.7    10568372        153908
[PB Error 2024-Dec-12 19:11:56][src/vcfWriter.cpp:1116] Logic error: Interval end (181 != VariantContext start - 1 (0, exiting.
[PB Error 2024-Dec-12 19:11:56][src/assembleRegions_GPU.cu:1712] cudaSafeCall() failed: driver shutting down, exiting.
2

Parabricks version: 4.7.1-1
Container: nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1
Execution method: singularity
GPU: 5090
NVIDIA driver: 595.84
System RAM: 512G

[PB Info 2026-Aug-15 17:42:26] NC_056480.1:10233601	3.5	4789772	1368506
[PB Info 2026-Aug-15 17:42:36] NC_056481.1:9916801	3.7	5027510	1371139
[PB Info 2026-Aug-15 17:42:46] NC_056482.1:9384001	3.8	5254724	1370797
[PB Info 2026-Aug-15 17:42:56] NC_056483.1:9129601	4.0	5475952	1368988
[PB Info 2026-Aug-15 17:43:06] NC_056484.1:7862401	4.2	5681367	1363528
[PB Info 2026-Aug-15 17:43:16] NC_056485.1:8774401	4.3	5893764	1360099
[PB Info 2026-Aug-15 17:43:26] NC_056486.1:13334401	4.5	6101619	1355915
[PB Info 2026-Aug-15 17:43:36] NW_024622969.1:1	4.7	6335733	1357657
[PB Info 2026-Aug-15 17:43:46] NW_024632471.1:1	4.8	6538555	1352804
[PB Error 2026-Aug-15 17:43:52][src/vcfWriter.cpp:910] Logic error: Interval end (348 != VariantContext start - 1 (0, exiting.

I’m experiencing the same issue in version 4.7.1.1. Has there been any progress on this?

3

Hello,

Thanks for reaching out. We haven’t been able to reproduce this issue from our end. Could you please share the full command and log file with passing flag “–x3” and “–verbose” with us? If by any chance that you can share your input data with us, that would be very helpful for our debugging too.

Thanks.

4

sampletest.log (3.6 MB)

Attached the log. Thanks in advance for checking it out.

5

Thanks for sharing the log file. The command and debug messages look fine. It seems to be a corner case that we are handling properly.

Could you please share your input data with us if possible? Ideally the fasta and the bam with a few chromosomes at the beginning that can reproduce the error. If it’s public data, a link to it would be enough.

Thanks.

6

The fasta is https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/729/295/GCF_008729295.1_YSFRI_Pleo_2.0/GCF_008729295.1_YSFRI_Pleo_2.0_genomic.fna.gz

And the bam is attached. Thanks!

part.bam.gz (771.4 KB)

7

Thank you so much for sharing the data! Confirmed that we can reproduce the issue, and it has been fixed. This update will be included in the coming 4.8 release in Oct.

Thanks again for your support.