Hi,
I use gatk4 to call gvcf, but it is too slowly than gatk3.8, and have so many WARN. What should I do?
Below is the command and stdout.
[node1 whzhang:~]$ gatk-launch HaplotypeCaller -R data/apple/reference_genome/apple_index_GATK/GDDH13_1-1_formatted.fasta -I 0010.bam -O 0010.g.vcf -ERC GVCF
Using GATK jar /store/whzhang/anaconda2/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-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=1 -jar /store/whzhang/anaconda2/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar HaplotypeCaller -R data/apple/reference_genome/apple_index_GATK/GDDH13_1-1_formatted.fasta -I 0010.bam -O 0010.g.vcf -ERC GVCF
08:16:07.614 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/store/whzhang/anaconda2/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
08:16:07.740 INFO HaplotypeCaller - ------------------------------------------------------------
08:16:07.740 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.0.0
08:16:07.740 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
08:16:07.740 INFO HaplotypeCaller - Executing as whzhang@node1 on Linux v4.4.0-109-generic amd64
08:16:07.741 INFO HaplotypeCaller - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_121-b15
08:16:07.741 INFO HaplotypeCaller - Start Date/Time: January 16, 2018 8:16:07 AM EST
08:16:07.741 INFO HaplotypeCaller - ------------------------------------------------------------
08:16:07.741 INFO HaplotypeCaller - ------------------------------------------------------------
08:16:07.741 INFO HaplotypeCaller - HTSJDK Version: 2.13.2
08:16:07.741 INFO HaplotypeCaller - Picard Version: 2.17.2
08:16:07.741 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 1
08:16:07.741 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
08:16:07.741 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
08:16:07.741 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
08:16:07.742 INFO HaplotypeCaller - Deflater: IntelDeflater
08:16:07.742 INFO HaplotypeCaller - Inflater: IntelInflater
08:16:07.742 INFO HaplotypeCaller - GCS max retries/reopens: 20
08:16:07.742 INFO HaplotypeCaller - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
08:16:07.742 INFO HaplotypeCaller - Initializing engine
08:16:08.173 INFO HaplotypeCaller - Done initializing engine
08:16:08.178 INFO HaplotypeCallerEngine - Standard Emitting and Calling confidence set to 0.0 for reference-model confidence output
08:16:08.178 INFO HaplotypeCallerEngine - All sites annotated with PLs forced to true for reference-model confidence output
08:16:09.003 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/store/whzhang/anaconda2/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
08:16:09.004 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/store/whzhang/anaconda2/share/gatk4-4.0.0.0-0/gatk-package-4.0.0.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
08:16:09.049 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
08:16:09.049 INFO IntelPairHmm - Available threads: 24
08:16:09.049 INFO IntelPairHmm - Requested threads: 4
08:16:09.049 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
08:16:09.101 INFO ProgressMeter - Starting traversal
08:16:09.101 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
08:16:10.074 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:10.074 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:16.465 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:16.465 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:16.541 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:16.541 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:16.541 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:16.542 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:17.520 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:17.520 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:17.521 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:17.521 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:19.328 INFO ProgressMeter - Chr11:78484 0.2 530 3109.7
08:16:22.641 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:22.641 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:22.641 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:22.641 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:16:36.482 INFO ProgressMeter - Chr11:156253 0.5 1120 2454.3
08:16:51.222 INFO ProgressMeter - Chr11:157866 0.7 1130 1609.6
08:17:05.531 INFO ProgressMeter - Chr11:159791 0.9 1140 1212.1
08:17:06.944 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:06.944 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:08.300 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:08.300 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:08.300 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:08.300 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:08.300 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:08.302 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:08.302 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:08.302 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:15.814 INFO ProgressMeter - Chr11:214858 1.1 1550 1394.0
08:17:16.111 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:16.111 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:17.058 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:17.058 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.562 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.562 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.562 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.562 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.563 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.563 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.563 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.563 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.564 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.564 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.564 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.564 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.565 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:22.565 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:25.852 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:25.852 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:25.852 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:25.852 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:25.867 INFO ProgressMeter - Chr11:262343 1.3 1920 1500.7
08:17:27.890 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:27.890 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:27.890 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:27.890 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:32.182 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:32.182 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:32.183 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:32.183 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:32.709 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:32.709 WARN StrandBiasBySample - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
08:17:36.079 INFO ProgressMeter - Chr11:312783 1.4 2320 1600.4