java.nio.bufferunderflowexception haplotypecaller error for bqsr reads

Question

[analyst]

I got java.nio.bufferunderflowexception error while running haplotypeCaller on bqsr reads. However haplotypeCaller works fine for deduplicated reads (without bqsr).

I observed ApplyBQSR step generated warning (Zero bytes written).

Your suggestion are highly welcome

[Pierre Lindenbaum]

command is missing, version is missing.

[analyst]

GATK version:

The Genome Analysis Toolkit (GATK) v4.2.1.0

HTSJDK Version: 2.24.1

Picard Version: 2.25.4

COMMAND FOR BQSR

step 1: building the model

java -jar -Xmx50G gatk.jar BaseRecalibrator -I input.bam -R whaet.fa --known-sites wheat.vcf -O input.table --create-output-bam-index false

step 2: apply bqsr

java -jar -Xmx50G gatk.jar ApplyBQSR -I input.bam -R wheat.fa --bqsr-recal-file input.table -O input_bqsr.bam --create-output-bam-index false

COMMAND FOR VARIANT CALLING

java -jar -Xmx50G gatk.jar HaplotypeCaller --native-pair-hmm-threads 80 --sample-ploidy 6 -R wheat.fa -I input_bqsr.bam -O input_raw_variants.vcf