Error when running HaplotypeCaller

Hi,

I'm trying to call variants on WGS data using the following command (on a high-performance cluster using 4 cores per job) :

java -Xmx6G -jar $CLASSPATH -T HaplotypeCaller --dbsnp GRCh37-lite.vcf -nct 4 -R GRCh37-lite.fa -I /user/data/gent/gvo000/gvo00027/vsc40035/StJude/001/001_D.bam -maxAltAlleles 10 --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o 001_D.vcf

$CLASSPATH contains the location of the .jar file.

For 20 out of 70 samples the script ended without a problem, for the other 50 samples the same error messages was returned, given below. Can you tell what's going wrong?

Kind regards, Steve

INFO 07:28:05,514 ProgressMeter - 2:92269030 2.49e+08 3.1 h 44.0 s 11.0% 27.9 h 24.8 h INFO 07:29:05,515 ProgressMeter - 2:92309304 2.49e+08 3.1 h 44.0 s 11.0% 28.1 h 25.0 h INFO 07:30:05,516 ProgressMeter - 2:92320228 2.49e+08 3.1 h 44.0 s 11.0% 28.2 h 25.1 h INFO 07:30:06,052 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------

ERROR stack trace

java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:443) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:417) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.calculateGLsForThisEvent(GenotypingEngine.java:385) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoods(GenotypingEngine.java:222) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:880) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:141) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704) at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:745)

ERROR ------------------------------------------------------------------------------------------

ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):

ERROR

ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.

ERROR If not, please post the error message, with stack trace, to the GATK forum.

ERROR Visit our website and forum for extensive documentation and answers to

ERROR commonly asked questions http://www.broadinstitute.org/gatk

ERROR

ERROR MESSAGE: Code exception (see stack trace for error itself)

ERROR ------------------------------------------------------------------------------------------