Hi I'm trying to do a multisample variant call using several bam files in the following cmd
/mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk HaplotypeCaller -R /mnt/fastdata/md1jale/reference/hs37d5.fa -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24811_1#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24150_1#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24144_2#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24712_6#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24811_2#1.bam -O /mnt/fastdata/md1jale/WGS_MShef7_iPS/output/raw_variants.vcf
Using GATK jar /mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk-package-4.0.1.0-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 /mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk-package-4.0.1.0-local.jar HaplotypeCaller -R /mnt/fastdata/md1jale/reference/hs37d5.fa -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24811_1#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24150_1#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24144_2#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24712_6#1.bam -I /mnt/fastdata/md1jale/WGS_MShef7_iPS/24811_2#1.bam -O /mnt/fastdata/md1jale/WGS_MShef7_iPS/output/mshef7_wt_vs_ips_raw_variants.vcf
10:26:29.719 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk-package-4.0.1.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
10:26:29.935 INFO HaplotypeCaller - ------------------------------------------------------------
10:26:29.935 INFO HaplotypeCaller - The Genome Analysis Toolkit (GATK) v4.0.1.0
10:26:29.935 INFO HaplotypeCaller - For support and documentation go to https://software.broadinstitute.org/gatk/
10:26:29.935 INFO HaplotypeCaller - Executing as md1jale@sharc-node122.shef.ac.uk on Linux v3.10.0-693.11.6.el7.x86_64 amd64
10:26:29.936 INFO HaplotypeCaller - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_102-b14
10:26:29.936 INFO HaplotypeCaller - Start Date/Time: 14 February 2018 10:26:29 GMT
10:26:29.936 INFO HaplotypeCaller - ------------------------------------------------------------
10:26:29.936 INFO HaplotypeCaller - ------------------------------------------------------------
10:26:29.936 INFO HaplotypeCaller - HTSJDK Version: 2.14.1
10:26:29.936 INFO HaplotypeCaller - Picard Version: 2.17.2
10:26:29.937 INFO HaplotypeCaller - HTSJDK Defaults.COMPRESSION_LEVEL : 1
10:26:29.937 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
10:26:29.937 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
10:26:29.937 INFO HaplotypeCaller - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
10:26:29.937 INFO HaplotypeCaller - Deflater: IntelDeflater
10:26:29.937 INFO HaplotypeCaller - Inflater: IntelInflater
10:26:29.937 INFO HaplotypeCaller - GCS max retries/reopens: 20
10:26:29.937 INFO HaplotypeCaller - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
10:26:29.937 INFO HaplotypeCaller - Initializing engine
10:26:30.520 INFO HaplotypeCaller - Done initializing engine
10:26:30.528 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
10:26:31.119 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk-package-4.0.1.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
10:26:31.154 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/mnt/fastdata/md1jale/software/gatk-4.0.1.0/gatk-package-4.0.1.0-local.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
10:26:31.259 WARN IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
10:26:31.259 INFO IntelPairHmm - Available threads: 16
10:26:31.259 INFO IntelPairHmm - Requested threads: 4
10:26:31.259 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
10:26:31.298 INFO ProgressMeter - Starting traversal
10:26:31.298 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
10:26:33.832 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
10:26:33.865 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
10:26:33.880 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
10:26:33.911 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
10:26:34.733 WARN DepthPerSampleHC - Annotation will not be calculated, genotype is not called or alleleLikelihoodMap is null
10:26:41.497 INFO ProgressMeter - 1:15485 0.2 80 470.6
Despite having slight memory issues with running the above, the now command runs on providing large amount of memory, although i do get lots of WARN DepthPerSampleHC. Is this normal?