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Hadoop error?

Hello,
I am trying to run GATK 4 on a cluster with human data (NA12878) but it seems there is a problem (maybe with hadoop install as the warning says?).
Below is the command line and error.

Thanks for any help you can provide!
Pierrick

/home/ghmpz/NA12878_Illumina/04_Calling/18_SNP_list_HG38_GATK > gatk HaplotypeCallerSpark -I /home/ghmpz/NA12878_Illumina/03_Mapping/03_Hg38_STAR/01_Output_local_mode/Aligned.out.bam.sorted.bam -R /Databases/GENOMES/Mammalia/Homo_sapiens/Genome/20170306_NIST_hg38build/GCA_000001405.15.1-22XYM.fa -O SNP_list_GATK.vcf -dontUseSoftClippedBases -DSTACK_TRACE_ON_USEREXCEPTION
Using GATK wrapper script /storage/gpfs/prg/gatk-protected/build/install/gatk-protected/bin/gatk-protected
Running:
/storage/gpfs/prg/gatk-protected/build/install/gatk-protected/bin/gatk-protected HaplotypeCallerSpark -I /home/ghmpz/NA12878_Illumina/03_Mapping/03_Hg38_STAR/01_Output_local_mode/Aligned.out.bam.sorted.bam -R /Databases/GENOMES/Mammalia/Homo_sapiens/Genome/20170306_NIST_hg38build/GCA_000001405.15.1-22XYM.fa -O SNP_list_GATK.vcf -dontUseSoftClippedBases -DSTACK_TRACE_ON_USEREXCEPTION
09:58:05.575 WARN IntelGKLUtils - Error starting process to check for AVX support : grep -i avx /proc/cpuinfo
09:58:05.582 WARN IntelGKLUtils - Error starting process to check for AVX support : grep -i avx /proc/cpuinfo
[June 20, 2017 9:58:05 AM CEST] org.broadinstitute.hellbender.tools.HaplotypeCallerSpark --output SNP_list_GATK.vcf --dbsnp /storage/gpfs/home/ghmpz/NA12878_Illumina/04_Calling/18_SNP_list_HG38_GATK/STACK_TRACE_ON_USEREXCEPTION --dontUseSoftClippedBases true --reference /Databases/GENOMES/Mammalia/Homo_sapiens/Genome/20170306_NIST_hg38build/GCA_000001405.15.1-22XYM.fa --input /home/ghmpz/NA12878_Illumina/03_Mapping/03_Hg38_STAR/01_Output_local_mode/Aligned.out.bam.sorted.bam --readShardSize 5000 --readShardPadding 100 --minAssemblyRegionSize 50 --maxAssemblyRegionSize 300 --assemblyRegionPadding 100 --activeProbabilityThreshold 0.002 --maxProbPropagationDistance 50 --group StandardAnnotation --group StandardHCAnnotation --GVCFGQBands 1 --GVCFGQBands 2 --GVCFGQBands 3 --GVCFGQBands 4 --GVCFGQBands 5 --GVCFGQBands 6 --GVCFGQBands 7 --GVCFGQBands 8 --GVCFGQBands 9 --GVCFGQBands 10 --GVCFGQBands 11 --GVCFGQBands 12 --GVCFGQBands 13 --GVCFGQBands 14 --GVCFGQBands 15 --GVCFGQBands 16 --GVCFGQBands 17 --GVCFGQBands 18 --GVCFGQBands 19 --GVCFGQBands 20 --GVCFGQBands 21 --GVCFGQBands 22 --GVCFGQBands 23 --GVCFGQBands 24 --GVCFGQBands 25 --GVCFGQBands 26 --GVCFGQBands 27 --GVCFGQBands 28 --GVCFGQBands 29 --GVCFGQBands 30 --GVCFGQBands 31 --GVCFGQBands 32 --GVCFGQBands 33 --GVCFGQBands 34 --GVCFGQBands 35 --GVCFGQBands 36 --GVCFGQBands 37 --GVCFGQBands 38 --GVCFGQBands 39 --GVCFGQBands 40 --GVCFGQBands 41 --GVCFGQBands 42 --GVCFGQBands 43 --GVCFGQBands 44 --GVCFGQBands 45 --GVCFGQBands 46 --GVCFGQBands 47 --GVCFGQBands 48 --GVCFGQBands 49 --GVCFGQBands 50 --GVCFGQBands 51 --GVCFGQBands 52 --GVCFGQBands 53 --GVCFGQBands 54 --GVCFGQBands 55 --GVCFGQBands 56 --GVCFGQBands 57 --GVCFGQBands 58 --GVCFGQBands 59 --GVCFGQBands 60 --GVCFGQBands 70 --GVCFGQBands 80 --GVCFGQBands 90 --GVCFGQBands 99 --indelSizeToEliminateInRefModel 10 --useAllelesTrigger false --dontTrimActiveRegions false --maxDiscARExtension 25 --maxGGAARExtension 300 --paddingAroundIndels 150 --paddingAroundSNPs 20 --kmerSize 10 --kmerSize 25 --dontIncreaseKmerSizesForCycles false --allowNonUniqueKmersInRef false --numPruningSamples 1 --recoverDanglingHeads false --doNotRecoverDanglingBranches false --minDanglingBranchLength 4 --consensus false --maxNumHaplotypesInPopulation 128 --errorCorrectKmers false --minPruning 2 --debugGraphTransformations false --kmerLengthForReadErrorCorrection 25 --minObservationsForKmerToBeSolid 20 --likelihoodCalculationEngine PairHMM --base_quality_score_threshold 18 --gcpHMM 10 --pair_hmm_implementation FASTEST_AVAILABLE --pcr_indel_model CONSERVATIVE --phredScaledGlobalReadMismappingRate 45 --nativePairHmmThreads 1 --useDoublePrecision false --debug false --useFilteredReadsForAnnotations false --emitRefConfidence NONE --bamWriterType CALLED_HAPLOTYPES --disableOptimizations false --justDetermineActiveRegions false --dontGenotype false --captureAssemblyFailureBAM false --errorCorrectReads false --doNotRunPhysicalPhasing false --min_base_quality_score 10 --useNewAFCalculator false --annotateNDA false --heterozygosity 0.001 --indel_heterozygosity 1.25E-4 --heterozygosity_stdev 0.01 --standard_min_confidence_threshold_for_calling 10.0 --max_alternate_alleles 6 --max_genotype_count 1024 --sample_ploidy 2 --genotyping_mode DISCOVERY --contamination_fraction_to_filter 0.0 --output_mode EMIT_VARIANTS_ONLY --allSitePLs false --readValidationStringency SILENT --interval_set_rule UNION --interval_padding 0 --interval_exclusion_padding 0 --bamPartitionSize 0 --disableSequenceDictionaryValidation false --shardedOutput false --numReducers 0 --sparkMaster local[*] --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false --disableToolDefaultReadFilters false --minimumMappingQuality 20
[June 20, 2017 9:58:05 AM CEST] Executing as ghmpz@ademons6511 on Linux 2.6.32-504.16.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_121-b13; Version: b4390fb-SNAPSHOT
09:58:05.583 INFO HaplotypeCallerSpark - HTSJDK Defaults.COMPRESSION_LEVEL : 1
09:58:05.583 INFO HaplotypeCallerSpark - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
09:58:05.583 INFO HaplotypeCallerSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
09:58:05.583 INFO HaplotypeCallerSpark - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
09:58:05.583 INFO HaplotypeCallerSpark - Deflater: JdkDeflater
09:58:05.583 INFO HaplotypeCallerSpark - Inflater: JdkInflater
09:58:05.583 INFO HaplotypeCallerSpark - Initializing engine
09:58:05.583 INFO HaplotypeCallerSpark - Done initializing engine
09:58:05.977 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
09:58:07.069 INFO HaplotypeCallerSpark - Shutting down engine
[June 20, 2017 9:58:07 AM CEST] org.broadinstitute.hellbender.tools.HaplotypeCallerSpark done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=842530816


A USER ERROR has occurred: null


Use -DSTACK_TRACE_ON_USEREXCEPTION to print the stack trace.

Tagged:

Issue · Github
by Sheila

Issue Number
2220
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

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