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 SRR7062654.md.bam -O SRR7062654.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 11:10:57.593 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 11:10:57.688 INFO BaseRecalibrator - ------------------------------------------------------------ 11:10:57.693 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.4.0.0 11:10:57.694 INFO BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:10:57.694 INFO BaseRecalibrator - Executing as formation@n024 on Linux v4.18.0-372.32.1.el8_6.x86_64 amd64 11:10:57.694 INFO BaseRecalibrator - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.6+9-LTS-190 11:10:57.694 INFO BaseRecalibrator - Start Date/Time: November 7, 2023 at 11:10:57 AM CET 11:10:57.694 INFO BaseRecalibrator - ------------------------------------------------------------ 11:10:57.694 INFO BaseRecalibrator - ------------------------------------------------------------ 11:10:57.696 INFO BaseRecalibrator - HTSJDK Version: 3.0.5 11:10:57.709 INFO BaseRecalibrator - Picard Version: 3.0.0 11:10:57.710 INFO BaseRecalibrator - Built for Spark Version: 3.3.1 11:10:57.710 INFO BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:10:57.711 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:10:57.711 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:10:57.711 INFO BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:10:57.712 INFO BaseRecalibrator - Deflater: IntelDeflater 11:10:57.712 INFO BaseRecalibrator - Inflater: IntelInflater 11:10:57.713 INFO BaseRecalibrator - GCS max retries/reopens: 20 11:10:57.713 INFO BaseRecalibrator - Requester pays: disabled 11:10:57.715 INFO BaseRecalibrator - Initializing engine 11:10:58.054 INFO FeatureManager - Using codec VCFCodec to read file file:///work/user/formation/Formation_Aln-SNP3/Gallus_gallus_incl_consequences_chr25-26.vcf 11:10:58.938 INFO BaseRecalibrator - Done initializing engine 11:10:58.945 INFO BaseRecalibrationEngine - The covariates being used here: 11:10:58.946 INFO BaseRecalibrationEngine - ReadGroupCovariate 11:10:58.946 INFO BaseRecalibrationEngine - QualityScoreCovariate 11:10:58.946 INFO BaseRecalibrationEngine - ContextCovariate 11:10:58.947 INFO BaseRecalibrationEngine - CycleCovariate 11:10:58.967 INFO ProgressMeter - Starting traversal 11:10:58.967 INFO ProgressMeter - Current Locus Elapsed Minutes Reads Processed Reads/Minute 11:11:09.017 INFO ProgressMeter - 25:1144034 0.2 132000 788687.5 11:11:19.012 INFO ProgressMeter - 26:123108 0.3 521000 1559568.9 11:11:29.026 INFO ProgressMeter - 26:1934107 0.5 970000 1936256.6 11:11:39.037 INFO ProgressMeter - 26:3599286 0.7 1440000 2156280.4 11:11:49.046 INFO ProgressMeter - 26:5276997 0.8 1909000 2287231.9 11:11:49.145 WARN IntelInflater - Zero Bytes Written : 0 11:11:49.158 INFO BaseRecalibrator - 19754 read(s) filtered by: MappingQualityNotZeroReadFilter 0 read(s) filtered by: MappingQualityAvailableReadFilter 0 read(s) filtered by: MappedReadFilter 0 read(s) filtered by: NotSecondaryAlignmentReadFilter 55182 read(s) filtered by: NotDuplicateReadFilter 0 read(s) filtered by: PassesVendorQualityCheckReadFilter 0 read(s) filtered by: WellformedReadFilter 74936 total reads filtered out of 1988606 reads processed 11:11:49.160 INFO ProgressMeter - 26:5311304 0.8 1913670 2287619.5 11:11:49.160 INFO ProgressMeter - Traversal complete. Processed 1913670 total reads in 0.8 minutes. 11:11:49.440 INFO BaseRecalibrator - Calculating quantized quality scores... 11:11:49.489 INFO BaseRecalibrator - Writing recalibration report... 11:11:54.202 INFO BaseRecalibrator - ...done! 11:11:54.206 INFO BaseRecalibrator - BaseRecalibrator was able to recalibrate 1913670 reads 11:11:54.207 INFO BaseRecalibrator - Shutting down engine [November 7, 2023 at 11:11:54 AM CET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.95 minutes. Runtime.totalMemory()=162267136