HaplotypeCaller java error

Question

[lmobuchon]

Dear colleagues,

I am trying to run HaplotypeCaller on ~180 WES on our cluster but I got error (see below). I am using Java 1.8.0_74 and GenomeAnalysisTK-3.1-1, and no multithread.

Thanks a lot for your help !

Lenha

Error:

##### ERROR -----------------------------------------------------------------------------------------
ERROR stack trace

java.lang.ExceptionInInitializerError
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.(GenomeAnalysisEngine.java:167)
at org.broadinstitute.sting.gatk.CommandLineExecutable.(CommandLineExecutable.java:57)
at org.broadinstitute.sting.gatk.CommandLineGATK.(CommandLineGATK.java:66)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:106)
Caused by: java.lang.NullPointerException
at org.reflections.Reflections.scan(Reflections.java:220)
at org.reflections.Reflections.scan(Reflections.java:166)
at org.reflections.Reflections.(Reflections.java:94)
at org.broadinstitute.sting.utils.classloader.PluginManager.(PluginManager.java:79)
... 4 more
##### 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 probl

em.
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 -----------------------------------------------------------------------------------------

[Pierre Lindenbaum]

what was the command line ? how about using a more recent version (e.g: 3.8 ?)

[lmobuchon]

This is the command line :

cmd="${JAVANEW} -Xmx40g -jar ${GATK} -T HaplotypeCaller -I ${BAM} -R ${GEN_REF} -dcov 100000 -o ${VCF} -stand_emit_conf ${STAND_EMIT_CONF} -stand_call_conf ${STAND_CALL_CONF} -A FisherStrand -A DepthPerAlleleBySample -A AlleleBalanceBySample -A HomopolymerRun -K ${GATK_KEY} -et NO_ET"

I launched it on a our compute cluster !

I will try with a more recent version as well !

Thanks a lot ! :)

[finswimmer]

Hello lmobuchon,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

Thank you!

[Pierre Lindenbaum]

hard to debug with all those ${} with unknown values....

[lmobuchon]

OK sorry; This is the whole command line:

MAINDIR="/path/to/my/home"
INFOFILE="${MAINDIR}/dbGap_data/Melanoma_CTLA4/SRR_Acc_List.txt"
BAMDIR="${MAINDIR}/dbGap_data/ncbi/dbGaP-11376/files/BAM_Melanoma_CTLA4"
VCFDIR="${MAINDIR}/dbGap_data/ncbi/dbGaP-11376/files/VCF_Melanoma_CTLA4"
JAVANEW="${MAINDIR}/bin/jre1.8.0_181/bin/java"
GATK="/path/bioinfo/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar"
GATK_KEY="/path/bioinfo/ngs-data-analysis/ewok_0.2/bioinfo_platform_curie.fr.key"
LOD=5
GEN_REF="/path/to/human/ref"

STAND_CALL_CONF=30
STAND_EMIT_CONF=10
torqueOut="${VCFDIR}/torque"
torqueErr="${VCFDIR}/torque"

while read p
    do
BAM="${BAMDIR}/${p}_sorted_duplicates_removed.bam"
VCF="${VCFDIR}/${p}.vcf"

cmd="${JAVANEW} -Xmx40g -jar ${GATK} -T HaplotypeCaller -I ${BAM} -R ${GEN_REF} -dcov 100000 -o ${VCF} -stand_emit_conf ${STAND_EMIT_CONF} -stand_call_conf ${STAND_CALL_CONF} -A FisherStrand -A DepthPerAlleleBySample -A AlleleBalanceBySample -A HomopolymerRun -K ${GATK_KEY} -et NO_ET"

caller=`echo "${cmd}" | \
qsub \
-q batch \
-l walltime=10:00:00 \
-l nodes=1:ppn=1 \
-l mem=40gb \
-o ${torqueOut} \
-e ${torqueErr} \
-m abe \
-N HaplotypeCaller_${p}`
echo "${p} : ${caller}"
done < ${INFOFILE}

I tried without the loop as well but it didn't work !

[lmobuchon]

I tried with the latest version of java and I get the same error ! :( Lenha

[Pierre Lindenbaum]

and the lastest version of gatk ?