Dear GATK Team,
I'm trying to run HaplotypeCaller, on a Bowtie2 bam file, but I'm having a Code exception.
Any idea how to fix it?
Best regards,
Miguel Machado
Command:
/scratch/mpmachado/NGStools/java_oracle/jre1.8.0_45/bin/java -jar /scratch/mpmachado/NGStools/gatk/GenomeAnalysisTK.jar -T HaplotypeCaller -R /scratch/mpmachado/trabalho1diversidade/genomaReferencia/dadosGenoma/NC_004368.fna -I /scratch/mpmachado/trabalho1diversidade/genomaReferencia/outputs/bowtie/GBS_01.sorted_position.bam --out output.raw.snps.indels.vcf --genotyping_mode DISCOVERY --output_mode EMIT_ALL_SITES --sample_ploidy 1
INFO 16:21:59,507 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:21:59,511 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-0-g7e26428, Compiled 2015/05/15 03:25:41
INFO 16:21:59,511 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 16:21:59,511 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 16:21:59,516 HelpFormatter - Program Args: -T HaplotypeCaller -R /scratch/mpmachado/trabalho1diversidade/genomaReferencia/dadosGenoma/NC_004368.fna -I /scratch/mpmachado/trabalho1diversidade/genomaReferencia/outputs/bowtie/GBS_01.sorted_position.bam --out output.raw.snps.indels.vcf --genotyping_mode DISCOVERY --output_mode EMIT_ALL_SITES --sample_ploidy 1
INFO 16:21:59,521 HelpFormatter - Executing as mpmachado@dawkins on Linux 2.6.32-5-amd64 i386; Java HotSpot(TM) Server VM 1.8.0_45-b14.
INFO 16:21:59,521 HelpFormatter - Date/Time: 2015/07/07 16:21:59
INFO 16:21:59,521 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:21:59,521 HelpFormatter - --------------------------------------------------------------------------------
INFO 16:22:00,257 GenomeAnalysisEngine - Strictness is SILENT
INFO 16:22:00,360 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 500
INFO 16:22:00,370 SAMDataSource$SAMReaders - Initializing SAMRecords in serial
INFO 16:22:00,401 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03
INFO 16:22:00,410 HCMappingQualityFilter - Filtering out reads with MAPQ < 20
INFO 16:22:01,869 GATKRunReport - Uploaded run statistics report to AWS S3
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.NullPointerException
at java.util.TreeMap.compare(TreeMap.java:1290)
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)
