Abrubt no-error stops in HaplotypeCaller

[gevro]

Hi,
Running GATK 4.6.2.0. Very basic HaplotypeCaller run that just ends without completing and also without any error:

00:33:35.230 INFO  ProgressMeter -       chr12:69607084              4.4                 18980           4346.4 00:33:45.241 INFO  ProgressMeter -       chr12:69723593              4.5                 19730           4351.9 00:33:55.328 INFO  ProgressMeter -       chr12:69864855              4.7                 20580           4377.0 00:34:05.346 INFO  ProgressMeter -       chr12:69993114              4.9                 21360           4387.1 00:34:15.452 INFO  ProgressMeter -       chr12:70134697              5.0                 22190           4405.2 00:34:25.583 INFO  ProgressMeter -       chr12:70239416              5.2                 22820           4383.3 00:34:35.726 INFO  ProgressMeter -       chr12:70393729              5.4                 23690           4407.3 00:34:45.909 INFO  ProgressMeter -       chr12:70499000              5.5                 24270           4377.0 00:34:55.933 INFO  ProgressMeter -       chr12:70628174              5.7                 24970           4371.6 00:35:05.972 INFO  ProgressMeter -       chr12:70799439              5.9                 25880           4401.9

Using GATK jar /gpfs/data/lab/bin/gatk/gatk-package-4.6.2.0-local.jar Running:     java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx20g -jar /gpfs/data/lab/bin/gatk/gatk-package-4.6.2.0-local.jar HaplotypeCaller -I /dir/sample-X-X-M45-B001-idEKZUJ-pbmm2_1.13.0_GRCh38.aligned.sorted.aligned.bam -O /dir/sample-X-X-M45-B001-idEKZUJ-pbmm2_1.13.0_GRCh38.aligned.sorted.aligned.hc_shards/sample-X-X-M45-B001-idEKZUJ-pbmm2_1.13.0_GRCh38.aligned.sorted.aligned.GATK.g.0083.vcf.gz -R /gpfs/data/lab/reference-files/hg38/hg38.fa -L /dir/sample-X-X-M45-B001-idEKZUJ-pbmm2_1.13.0_GRCh38.aligned.sorted.aligned.intervals/0083-scattered.interval_list -ERC GVCF -G StandardAnnotation -G StandardHCAnnotation -G AS_StandardAnnotation

This keeps happening on this and about 5% of interval shards. Also happened on GATK 4.6.0.0 on the same input file.

And about half of these jobs seem to produce this error:

#
# A fatal error has been detected by the Java Runtime Environment:
#
#  SIGSEGV (0xb) at pc=0x000015555502f291, pid=734329, tid=734330
#
# JRE version: OpenJDK Runtime Environment (25.0+36) (build 25+36-3489)
# Java VM: OpenJDK 64-Bit Server VM (25+36-3489, mixed mode, sharing, tiered, compressed oops, compressed class ptrs, serial gc, linux-amd64)
# Problematic frame:
# C  [libc.so.6+0xcf291]  __memset_avx2_erms+0x11
#

I tried changing to the latest version of jdk (25) but not helping.

Thanks for any info on this GATK bug.