Using GATK jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-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=2 -Xmx7g -jar /usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar BaseRecalibrator -I SRR7062655.md.bam -O SRR7062655.md.recal.table --tmp-dir . -R Gallus_gallus.Gallus_gallus-5.0.dna.toplevel_chr25-26.fa --known-sites Gallus_gallus_incl_consequences_chr25-26.vcf --verbosity INFO 11:10:13.067 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/bioinfo/src/GATK/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 11:10:13.136 INFO BaseRecalibrator - ------------------------------------------------------------ 11:10:13.138 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.4.0.0 11:10:13.138 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:10:13.138 INFO BaseRecalibrator - Executing as formation@n024 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64 11:10:13.138 INFO BaseRecalibrator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.6+9-LTS-190 11:10:13.139 INFO BaseRecalibrator - Start Date/Time: November 7, 2023 at 11:10:12 AM CET 11:10:13.139 INFO BaseRecalibrator - ------------------------------------------------------------ 11:10:13.139 INFO BaseRecalibrator - ------------------------------------------------------------ 11:10:13.142 INFO BaseRecalibrator - HTSJDK Version: 3.0.5 11:10:13.142 INFO BaseRecalibrator - Picard Version: 3.0.0 11:10:13.143 INFO BaseRecalibrator - Built for Spark Version: 3.3.1 11:10:13.143 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:10:13.144 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:10:13.144 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:10:13.144 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:10:13.144 INFO BaseRecalibrator - Deflater: IntelDeflater 11:10:13.144 INFO BaseRecalibrator - Inflater: IntelInflater 11:10:13.145 INFO BaseRecalibrator - GCS max retries/reopens: 20 11:10:13.145 INFO BaseRecalibrator - Requester pays: disabled 11:10:13.146 INFO BaseRecalibrator - Initializing engine 11:10:13.433 INFO FeatureManager - Using codec VCFCodec to read file file:///work/user/formation/Formation_Aln-SNP3/Gallus_gallus_incl_consequences_chr25-26.vcf 11:10:14.078 INFO BaseRecalibrator - Done initializing engine 11:10:14.086 INFO BaseRecalibrationEngine - The covariates being used here: 11:10:14.087 INFO BaseRecalibrationEngine - ReadGroupCovariate 11:10:14.088 INFO BaseRecalibrationEngine - QualityScoreCovariate 11:10:14.089 INFO BaseRecalibrationEngine - ContextCovariate 11:10:14.089 INFO BaseRecalibrationEngine - CycleCovariate 11:10:14.106 INFO ProgressMeter - Starting traversal 11:10:14.107 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute 11:10:24.118 INFO ProgressMeter - 25:2293989 0.2 349000 2093372.0 11:10:34.113 INFO ProgressMeter - 26:2326004 0.3 1016000 3047238.2 11:10:44.114 INFO ProgressMeter - 26:4896021 0.5 1714000 3427314.5 11:10:45.729 WARN IntelInflater - Zero Bytes Written : 0 11:10:45.759 INFO BaseRecalibrator - 19170 read(s) filtered by: MappingQualityNotZeroReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 86461 read(s) filtered by: NotDuplicateReadFilter 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 0 read(s) filtered by: WellformedReadFilter 105631 total reads filtered out of 1921919 reads processed 11:10:45.762 INFO ProgressMeter - 26:5312231 0.5 1816288 3442656.1 11:10:45.762 INFO ProgressMeter - Traversal complete. Processed 1816288 total reads in 0.5 minutes. 11:10:46.011 INFO BaseRecalibrator - Calculating quantized quality scores... 11:10:46.059 INFO BaseRecalibrator - Writing recalibration report... 11:10:49.588 INFO BaseRecalibrator - ...done! 11:10:49.591 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 1816288 reads 11:10:49.592 INFO BaseRecalibrator - Shutting down engine [November 7, 2023 at 11:10:49 AM CET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.61 minutes. Runtime.totalMemory()=162267136