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A JAVA & Haplotype question

Hello! This is the 1st time I used GATK4.0.4.0 ,and I met something puzzled me a lot.
the CMD is
$GATK HaplotypeCaller -R $GENOME -I $sample-md_rl.bam -O $sample.g.vcf -ERC GVCF

And I got these lines,

Using GATK jar /home/gaotiangang/niuguohao/biosoft/GATK4/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/gaotiangang/niuguohao/biosoft/GATK4/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar HaplotypeCaller -R /home/gaotiangang/niuguohao/201806call/new_2k_genome/eggawk.second.fill.2k.fasta -I seq103-md_rl.bam -O seq103.g.vcf -ERC GVCF
Picked up _JAVA_OPTIONS: -Xmx40960m -Xms40960m
15:38:22.844 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/gaotiangang/niuguohao/biosoft/GATK4/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
15:38:23.897 INFO HaplotypeCaller - ------------------------------------------------------------
15:38:23.897 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.4.0
15:38:23.898 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
15:38:23.898 INFO HaplotypeCaller - Executing as [email protected] on Linux v2.6.32-358.el6.x86_64 amd64
15:38:23.898 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_72-b15
15:38:23.899 INFO HaplotypeCaller - Start Date/Time: June 27, 2018 3:38:22 PM CST
15:38:23.899 INFO HaplotypeCaller - ------------------------------------------------------------
15:38:23.899 INFO HaplotypeCaller - ------------------------------------------------------------
15:38:23.900 INFO HaplotypeCaller - HTSJDK Version: 2.14.3
15:38:23.900 INFO HaplotypeCaller - Picard Version: 2.18.2
15:38:23.900 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:38:23.900 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:38:23.900 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:38:23.901 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:38:23.901 INFO HaplotypeCaller - Deflater: IntelDeflater
15:38:23.901 INFO HaplotypeCaller - Inflater: IntelInflater
15:38:23.901 INFO HaplotypeCaller - GCS max retries/reopens: 20
15:38:23.901 INFO HaplotypeCaller - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
15:38:23.901 INFO HaplotypeCaller - Initializing engine
15:38:26.258 INFO HaplotypeCaller - Done initializing engine
15:38:26.398 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
15:38:26.399 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
15:38:27.239 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/gaotiangang/niuguohao/biosoft/GATK4/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
15:38:27.332 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/gaotiangang/niuguohao/biosoft/GATK4/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
15:38:27.363 WARN NativeLibraryLoader - Unable to load libgkl_pairhmm_omp.so from native/libgkl_pairhmm_omp.so (/tmp/niuguohao/libgkl_pairhmm_omp7066111566211046687.so: /usr/lib64/libgomp.so.1: version `GOMP_4.0' not found (required by /tmp/niuguohao/libgkl_pairhmm_omp7066111566211046687.so))
15:38:27.363 INFO PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported
15:38:27.363 INFO NativeLibraryLoader - Loading libgkl_pairhmm.so from jar:file:/home/gaotiangang/niuguohao/biosoft/GATK4/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm.so
15:38:27.441 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
15:38:27.442 WARN IntelPairHmm - Ignoring request for 4 threads; not using OpenMP implementation
15:38:27.442 INFO PairHMM - Using the AVX-accelerated native PairHMM implementation
15:38:27.560 INFO ProgressMeter - Starting traversal
15:38:27.561 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
15:38:38.859 INFO ProgressMeter - scaffold50:94431 0.2 650 3451.9
15:38:49.130 INFO ProgressMeter - scaffold73:7654 0.4 1180 3282.5
15:38:59.895 INFO ProgressMeter - scaffold73:47575 0.5 1510 2802.0
15:39:10.435 INFO ProgressMeter - scaffold73:98123 0.7 1940 2714.9
15:39:20.496 INFO ProgressMeter - scaffold73:166675 0.9 2550 2890.3
15:39:30.567 INFO ProgressMeter - scaffold55:75112 1.1 2960 2818.8
15:39:32.195 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
15:39:32.195 WARN** StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
**15:39:32.268 WARN ** DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
**15:39:32.269 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
15:39:32.269 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
15:39:32.269 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
15:39:32.270 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
15:39:32.270 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
15:39:42.073 INFO ProgressMeter - scaffold21:122916 1.2 4120 3317.6
15:39:52.624 INFO ProgressMeter - scaffold21:252699 1.4 5000 3544.4

So ,I want to know the meaning of "StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null"? Is there anything wrong with my data ?

Thanks a lot!

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