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GENOTYPE_GIVEN_ALLELES mode not work in GATK4 beta

Hi, guys, I tried to run GGA(GENOTYPE_GIVEN_ALLELES) of GATK4.beta.1, but failed with NullPointerException, I'm sure that my input file and parameter settings are OK, cause I have checked my setting with this post of our forum and 4.beta.1's docs, also the equivalent parameters work fine for GATK3.7.

I haven't tested GGA with 4.beta.3 and 4.beta.2, as the release notes shows that there is no update related to this function. I'm wondering if GGA can function well for 4.beta or the future general release or maybe I need to change my parameters to get it running up? Below is my parameters and error log.

gatk-launch --javaOptions "-Xmx4g" HaplotypeCaller  \
   -R /reference/BWAIndex/genome.fa \
   -I  miseq_161113_PE75.bwa.sorted.filtered.recal.bam \
   -O miseq_161113_PE75_gatk4_pgkb.vcf \
   -L  /path/to/my.vcf.gz \
   --alleles /path/to/my.vcf.gz \
   --genotyping_mode GENOTYPE_GIVEN_ALLELES 
[July 14, 2017 2:51:14 PM CST] Executing as [email protected] on Linux 4.4.0-83-generic amd64; OpenJDK 64-Bit Server VM 1.8.0_131-8u131-b11-0ubuntu1.16.04.2-b11; Version: 4.beta.1
14:51:14.936 INFO  HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 1
14:51:14.936 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
14:51:14.936 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
14:51:14.936 INFO  HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
14:51:14.936 INFO  HaplotypeCaller - Deflater: IntelDeflater
14:51:14.936 INFO  HaplotypeCaller - Inflater: IntelInflater
14:51:14.936 INFO  HaplotypeCaller - Initializing engine
14:51:15.342 INFO  IntervalArgumentCollection - Processing 43 bp from intervals
14:51:15.350 INFO  HaplotypeCaller - Done initializing engine
14:51:15.356 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
14:51:15.594 WARN  PossibleDeNovo - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
14:51:15.737 WARN  PossibleDeNovo - Annotation will not be calculated, must provide a valid PED file (-ped) from the command line.
14:51:15.964 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/media/home/jiecui/software/gatk/gatk-4.beta.1/gatk-package-4.beta.1-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
[INFO] Available threads: 40
[INFO] Requested threads: 4
[INFO] Using 4 threads
14:51:16.035 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
14:51:16.051 INFO  ProgressMeter - Starting traversal
14:51:16.051 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Regions Processed   Regions/Minute
log4j:WARN No appenders could be found for logger (org.broadinstitute.hellbender.utils.MathUtils$Log10Cache).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
14:51:16.424 INFO  VectorLoglessPairHMM - Time spent in setup for JNI call : 0.001359444
14:51:16.424 INFO  PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.004590645
14:51:16.424 INFO  HaplotypeCaller - Shutting down engine
[July 14, 2017 2:51:16 PM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.03 minutes.
        at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerGenotypingEngine.createAlleleMapper(AssemblyBasedCallerGenotypingEngine.java:159)
        at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:128)
        at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:541)
        at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:221)
        at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:244)
        at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:217)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:838)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:115)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:170)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:189)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:131)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:152)
        at org.broadinstitute.hellbender.Main.main(Main.java:230)

Java and GATK version:

Java version: openjdk version "1.8.0_131"
GATK version: 4.beta.1

Issue · Github
by Sheila

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