GATK "Code exception"

[memento]

I tried to run GATK after alignment with bowtie - file was SortSam'ed and ReorderSam'ed (both picard) prior to GATK.

java -Xmx3g -jar GATK/GenomeAnalysisTK.jar -R ucsc.hg19.fasta -T UnifiedGenotyper -I file_in.bam --dbsnp dbsnp_132.hg19.vcf -o file_in_out.vcf -metrics snps.metrics -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 1000 -A DepthOfCoverage -A AlleleBalance -L hg19_exons.bed


Error:

INFO 20:39:02,940 HelpFormatter - Date/Time: 2012/02/06 20:39:02
INFO 20:39:02,940 HelpFormatter - ---------------------------------------------------------------------------------
INFO 20:39:02,940 HelpFormatter - ---------------------------------------------------------------------------------
INFO 20:39:02,956 RodBindingArgumentTypeDescriptor - Dynamically determined type of dbsnp_132.hg19.vcf to be VCF
INFO 20:39:02,966 GenomeAnalysisEngine - Strictness is SILENT
INFO 20:39:03,022 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 20:39:03,036 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.01
INFO 20:39:03,045 RMDTrackBuilder - Loading Tribble index from disk for file dbsnp_132.hg19.vcf
INFO 20:39:05,881 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.NullPointerException
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.getNextOverlappingBAMScheduleEntry(BAMScheduler.java:259)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.advance(BAMScheduler.java:170)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.populateFilteredIntervalList(BAMScheduler.java:99)
at org.broadinstitute.sting.gatk.datasources.reads.BAMScheduler.createOverIntervals(BAMScheduler.java:74)
at org.broadinstitute.sting.gatk.datasources.reads.IntervalSharder.shardOverIntervals(IntervalSharder.java:58)
at org.broadinstitute.sting.gatk.datasources.reads.SAMDataSource.createShardIteratorOverIntervals(SAMDataSource.java:1148)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getShardStrategy(GenomeAnalysisEngine.java:452)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:230)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:90)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 1.4-24-g6ec686b):
##### ERROR
##### ERROR Please visit the wiki to see if this is a known problem
##### ERROR If not, please post the error, with stack trace, to the GATK forum
##### ERROR Visit our wiki for extensive documentation http://www.broadinstitute.org/gsa/wiki
##### ERROR Visit our forum to view answers to commonly asked questions http://getsatisfaction.com/gsa
##### ERROR
##### ERROR MESSAGE: Code exception (see stack trace for error itself)
##### ERROR --------------------------------------------------------------------



Any ideas what could have caused that ?

[Bukowski]

Do what is says on the tin, go to http://getsatisfaction.com/gsa and check the forums - we've hit issues and found them already solved there, or acknowledged. If not the developers are very responsive.

That looks like quite a recent version of GATK, we've learned here that slavishly following the GATK release cycle just leads to problems. Pick a version that works, stick to it, keep and eye on the changelog on github to see if any essential features have been added or bugs fixed.

We had issues with the entire 1.3 release set, and once we established GenomeAnalysisTK-1.4-7-gc96fee4 fixed our problems - that's where we have left things. If you're using the GATK heavily you need to test each release thoroughly before introducing it into a production pipeline.

[NGSfan]

Do what is says on the tin, go to http://getsatisfaction.com/gsa and check the forums - we've hit issues and found them already solved there, or acknowledged. If not the developers are very responsive.

That looks like quite a recent version of GATK, we've learned here that slavishly following the GATK release cycle just leads to problems. Pick a version that works, stick to it, keep and eye on the changelog on github to see if any essential features have been added or bugs fixed.

We had issues with the entire 1.3 release set, and once we established GenomeAnalysisTK-1.4-7-gc96fee4 fixed our problems - that's where we have left things. If you're using the GATK heavily you need to test each release thoroughly before introducing it into a production pipeline.

I concur... I have encountered many problems by upgrading. I am on v1.2 for now. Will consider upgrading to 1.4 now that it seems more stable.