Hi, I'm still new to bioinformatics so I'll apologise in advance if I've made an obvious error anywhere here... I am running HaplotypeCaller on four species of rodent (Mus musculus and three wild, non-model species), with 12 individual bam files in each.
It works fine for Mus, but for one of the non-model species it ran for 18 days, then crashed at 90%; only then did I realise I speed things up by passing it a file of only the exonic intervals I'm interested in. However, when I try running it with the interval file I get the following error:
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.NullPointerException at java.util.ComparableTimSort.countRunAndMakeAscending(ComparableTimSort.java:295) at java.util.ComparableTimSort.sort(ComparableTimSort.java:171) at java.util.ComparableTimSort.sort(ComparableTimSort.java:146) at java.util.Arrays.sort(Arrays.java:472) at java.util.Collections.sort(Collections.java:155) at org.broadinstitute.sting.utils.interval.IntervalUtils.sortAndMergeIntervals(IntervalUtils.java:254) at org.broadinstitute.sting.utils.interval.IntervalUtils.getIntervalsWithFlanks(IntervalUtils.java:805) at org.broadinstitute.sting.utils.interval.IntervalUtils.loadIntervals(IntervalUtils.java:612) at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalBindingsPair(IntervalUtils.java:587) at org.broadinstitute.sting.utils.interval.IntervalUtils.parseIntervalArguments(IntervalUtils.java:549) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.initializeIntervals(GenomeAnalysisEngine.java:721) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:287) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)
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 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 ------------------------------------------------------------------------------------------
The code I used is:
java -Xmx10g -jar ~/bin/GenomeAnalysisTK-3.1-1/GenomeAnalysisTK.jar \ -T HaplotypeCaller \ -nct 10 \ -R ~/REF.fasta \ --intervals INTERVALS.bed \ --interval_padding 20 \ -log LOGFILE.log \ -I 1.bam \ -I 2.bam \ -I 3.bam \ -I 4.bam \ -I 5.bam \ -I 6.bam \ -I 7.bam \ -I 8.bam \ -I 9.bam \ -I 10.bam \ -I 11.bam \ -I 12.bam \ -o OUT.vcf
It works fine without the interval file, but I don't want to risk it taking three weeks and crashing again; so I think I need to include the intervals to speed things up. The BED file I use for the interval file is simply formatted as :
scaffold2617 357126 357876 scaffold2617 357876 357936 scaffold2617 357879 357936 etc.
Finally, as mentioned the code above works for Mus musculus, so there is obviously something different happening with my non-model species, but the BED file for each is formatted in exactly the same way....
Any help would be appreciated.