Hello,
I am trying to run the HaplotypeCaller and have run into a RunTime Error.
I am using GATK version 3.5-0-g36282e4
I am running the command as follows:
java -jar ~/packages/bin/GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R $ref \
-I $base.reads.bam \
--genotyping_mode DISCOVERY \
-stand_emit_conf 10 \
-stand_call_conf 30 \
-o $base.raw_variants.vcf
The full error is below:
INFO 10:48:23,416 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:48:23,419 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5-0-g36282e4, Compiled 2015/11/25 04:03:56
INFO 10:48:23,419 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 10:48:23,419 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 10:48:23,422 HelpFormatter - Program Args: -T HaplotypeCaller -R ref.fasta -I Gde_align.reads.bam --genotyping_mode DISCOVERY -stand_emit_conf 10 -stand_call_conf 30 -o Gde_align.raw_variants.vcf
INFO 10:48:23,428 HelpFormatter - Executing as jwolter1@c6220-7 on Linux 4.6.0-0.bpo.1-amd64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13.
INFO 10:48:23,429 HelpFormatter - Date/Time: 2016/08/12 10:48:23
INFO 10:48:23,429 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:48:23,429 HelpFormatter - --------------------------------------------------------------------------------
INFO 10:48:23,850 GenomeAnalysisEngine - Strictness is SILENT
INFO 10:48:23,964 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
INFO 10:48:23,973 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 10:48:23,997 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.02
INFO 10:48:24,004 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
INFO 10:48:24,008 GenomeAnalysisEngine - Reads file is unmapped. Skipping validation against reference.
INFO 10:48:24,567 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.NullPointerException
at java.util.TreeMap.compare(TreeMap.java:1294)
at java.util.TreeMap.put(TreeMap.java:538)
at java.util.TreeSet.add(TreeSet.java:255)
at org.broadinstitute.gatk.utils.sam.ReadUtils.getSAMFileSamples(ReadUtils.java:70)
at org.broadinstitute.gatk.engine.samples.SampleDBBuilder.addSamplesFromSAMHeader(SampleDBBuilder.java:66)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.initializeSampleDB(GenomeAnalysisEngine.java:846)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:296)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
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 ------------------------------------------------------------------------------------------
I don't know if this could be a factor but I am not confident that the reads in the bam have readgroup information. I had to add these artificially when doing DepthofCoverage on a different alignment.
Any help would be great appreciated.