Hi the team,

I have a "random" issue with the base recalibration step of my pipeline, occuring at the PrintReads step more precisely.

The command lines follow this pattern :

java -jar -Xmx4g GenomeAnalysisTK.jar -T BaseRecalibrator -nct 6 -R hg19.fa -knownSites dbSnp138.hg19.vcf.gz -I id.bam -o id.table

java -jar -Xmx4g GenomeAnalysisTK.jar -T PrintReads -nct 6 -R hg19.fa -I id.bam -BQSR id.table -o id_recal.bam

The error is this one :

A fatal error has been detected by the Java Runtime Environment:

#

Internal Error (safepoint.cpp:310), pid=74746, tid=0x00002b1e91c91700

guarantee(PageArmed == 0) failed: invariant

#

JRE version: Java(TM) SE Runtime Environment (8.0_92-b14) (build 1.8.0_92-b14)

The used versions of the different tools :
GATK 3.6
samtools 1.2
java 1.8

To be precise, I had also this problem on the 3.5 version.

Please, have you got an idea on what the error comes from ? Should I use a previous version of java ?

Thanks by advance for your help,
BPR