Variant calling HaplotypeCaller GATK

Question

[Hayler Edu]

Hello, I'm trying to do a variant calling using the Haplotypecaller tool of GATK but I have the next error.

20:35:42.387 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.531980043
20:35:42.387 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 10.258295356000001
20:35:42.387 INFO  SmithWatermanAligner - Total compute time in java Smith-Waterman : 54.48 sec
20:35:42.388 INFO  HaplotypeCaller - Shutting down engine
[September 6, 2022 at 8:35:42 PM COT] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 27.14 minutes.
Runtime.totalMemory()=3347054592
Exception in thread "main" java.lang.InternalError: a fault occurred in a recent unsafe memory access operation in compiled Java code

When I have the output the variant calling is only to chr5 but I need to chr21 and I don't know about the problem.

The pipeline that I'm using is the next:

gatk HaplotypeCaller -R /mnt/SSD1/Bases_de_datos_Edu/hg19.fa -I /media/HDD1/Edu/archivos_fastq/SEC9_BQSR.bam -L S04380219_Padded.bed
-stand-call-conf 30 -ploidy 4 --create-output-variant-index -O SEC9.vcf

[Pierre Lindenbaum]

a fault occurred in a recent unsafe memory access operation in compiled Java code:

https://stackoverflow.com/questions/45536049/java-lang-internalerror-a-fault-occurred-in-a-recent-unsafe-memory-access-opera

check you have enough space/memory , check IO