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 ?
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 ?
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