## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_62/LuC_62_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_62/LuC_62_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_62/LuC_62_dedup_metrics.txt CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Thu Aug 28 17:00:16 NOVT 2025 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE Unknown Library 205584 97115926 38495734 238752 165853 55371016 1037277 0.570404 48388971 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.003375 19658806 0 19774555 2.0 1.138222 9323099 538789 9358765 3.0 1.156345 5120920 89110 5119458 4.0 1.15878 2962474 37025 2946090 5.0 1.159108 1763173 17614 1740659 6.0 1.159152 1073463 8755 1051662 7.0 1.159158 664819 4729 644546 8.0 1.159158 416349 2628 400587 9.0 1.159159 264948 1547 251971 10.0 1.159159 169634 1017 159980 11.0 1.159159 110879 596 103046 12.0 1.159159 71836 389 66052 13.0 1.159159 46842 291 42806 14.0 1.159159 31582 210 28249 15.0 1.159159 20825 112 18444 16.0 1.159159 14109 110 12309 17.0 1.159159 9491 77 8177 18.0 1.159159 6482 56 5488 19.0 1.159159 4480 45 3723 20.0 1.159159 3147 38 2636 21.0 1.159159 2181 29 1788 22.0 1.159159 1499 21 1166 23.0 1.159159 1080 13 844 24.0 1.159159 758 20 539 25.0 1.159159 551 11 408 26.0 1.159159 382 4 263 27.0 1.159159 283 7 206 28.0 1.159159 212 7 136 29.0 1.159159 141 6 92 30.0 1.159159 105 0 68 31.0 1.159159 87 4 44 32.0 1.159159 55 3 41 33.0 1.159159 48 3 33 34.0 1.159159 28 2 16 35.0 1.159159 32 0 14 36.0 1.159159 20 0 9 37.0 1.159159 16 2 11 38.0 1.159159 12 0 7 39.0 1.159159 12 0 3 40.0 1.159159 7 0 3 41.0 1.159159 6 1 3 42.0 1.159159 5 0 1 43.0 1.159159 5 0 1 44.0 1.159159 3 0 1 45.0 1.159159 4 0 2 46.0 1.159159 2 0 0 47.0 1.159159 2 0 0 48.0 1.159159 0 0 0 49.0 1.159159 1 0 0 50.0 1.159159 0 1 0 51.0 1.159159 2 0 1 52.0 1.159159 1 0 0 53.0 1.159159 0 0 0 54.0 1.159159 0 0 0 55.0 1.159159 1 0 1 56.0 1.159159 2 0 0 57.0 1.159159 1 0 0 58.0 1.159159 0 0 0 59.0 1.159159 0 0 0 60.0 1.159159 0 0 1 61.0 1.159159 0 0 0 62.0 1.159159 0 0 0 63.0 1.159159 0 1 1 64.0 1.159159 0 0 1 65.0 1.159159 0 0 0 66.0 1.159159 0 0 1 67.0 1.159159 0 0 0 68.0 1.159159 1 0 0 69.0 1.159159 0 0 0 70.0 1.159159 1 0 0 71.0 1.159159 1 0 0 72.0 1.159159 0 0 0 73.0 1.159159 1 0 1 74.0 1.159159 0 0 0 75.0 1.159159 0 0 0 76.0 1.159159 0 0 0 77.0 1.159159 0 0 0 78.0 1.159159 0 0 0 79.0 1.159159 0 0 0 80.0 1.159159 0 0 0 81.0 1.159159 0 0 0 82.0 1.159159 0 0 0 83.0 1.159159 1 0 0 84.0 1.159159 0 0 0 85.0 1.159159 0 0 0 86.0 1.159159 0 0 0 87.0 1.159159 1 0 1 88.0 1.159159 0 0 0 89.0 1.159159 0 0 0 90.0 1.159159 0 0 0 91.0 1.159159 0 0 0 92.0 1.159159 0 0 0 93.0 1.159159 0 0 0 94.0 1.159159 0 0 0 95.0 1.159159 0 0 0 96.0 1.159159 0 0 0 97.0 1.159159 0 0 0 98.0 1.159159 0 0 0 99.0 1.159159 0 0 0 100.0 1.159159 0 0 0 103.0 0 1 0 0 115.0 0 1 0 0