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Old 08-26-2015, 05:36 AM   #1
Genomics101
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Location: Maryland, USA

Join Date: May 2012
Posts: 60
Default Can't run GATK HaplotypeCaller set ploidy = 1

Greetings!

I have been attempting to call variants on a haploid genome using GATK HaplotypeCaller, however when I set ploidy = 1, I get an error:

Code:
INFO 21:05:57,644 HelpFormatter - -------------------------------------------------------------------------------- 
INFO 21:05:57,648 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 
INFO 21:05:57,648 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO 21:05:57,651 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO 21:05:57,658 HelpFormatter - Program Args: -T HaplotypeCaller -R Ref.fa -I aln-pe_RG_sorted_dedup_realigned.bam -o aln-pe_RG_sorted_dedup_realigned_HC_ploidy1.vcf -ploidy 1 -maxAltAlleles 2 
INFO 21:05:57,666 HelpFormatter -on Linux 2.6.32-504.8.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_75-mockbuild_2015_01_20_23_39-b00. 
INFO 21:05:57,667 HelpFormatter - Date/Time: 2015/08/25 21:05:57 
INFO 21:05:57,667 HelpFormatter - -------------------------------------------------------------------------------- 
INFO 21:05:57,668 HelpFormatter - -------------------------------------------------------------------------------- 
INFO 21:05:57,913 GenomeAnalysisEngine - Strictness is SILENT 
INFO 21:05:58,027 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 
INFO 21:05:58,040 SAMDataSource$SAMReaders - Initializing SAMRecords in serial 
INFO 21:05:58,067 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 
INFO 21:05:58,079 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 
INFO 21:05:58,213 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files 
INFO 21:05:58,302 GenomeAnalysisEngine - Done preparing for traversal 
INFO 21:05:58,303 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO 21:05:58,305 ProgressMeter - | processed | time | per 1M | | total | remaining 
INFO 21:05:58,306 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime 
INFO 21:05:58,520 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units 
INFO 21:05:58,828 AFCalcFactory - Requested ploidy 1 maxAltAlleles 2 not supported by requested model EXACT_INDEPENDENT looking for an option 
INFO 21:05:58,829 AFCalcFactory - Selecting model EXACT_GENERAL_PLOIDY 
INFO 21:06:28,312 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s

ERROR stack trace
java.lang.NullPointerException
at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalc.assignGenotype(GeneralPloidyExactAFCalc.java:559)
at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalc.subsetAlleles(GeneralPloidyExactAFCalc.java:527)
at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:286)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:335)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:320)
at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:310)
at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.isActive(HaplotypeCaller.java:844)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.addIsActiveResult(TraverseActiveRegions.java:618)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.access$800(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.hasNext(TraverseActiveRegions.java:378)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268)
at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273)
at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
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:107)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
My arguments are set as follows:

Code:
-T HaplotypeCaller -R Ref.fa -I aln-pe_RG_sorted_dedup_realigned.bam -o aln-pe_RG_sorted_dedup_realigned_HC_ploidy1.vcf -ploidy 1 -maxAltAlleles 2
However it runs perfectly with ploidy = 2.

Any help is appreciated.
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Old 09-29-2015, 06:37 AM   #2
Clown_Bassie
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Location: Groningen

Join Date: Sep 2014
Posts: 2
Default

Did you try to run it with GATK 3.4 ?
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gatk, haploid, haplotypecaller, ploidy

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