## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LpS_3/LpS_3_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LpS_3/LpS_3_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LpS_3/LpS_3_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 17:00:18 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 336169 67233621 19440394 346131 227374 21508322 715636 0.320793 82826199 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.00698 31362327 0 31592642 2.0 1.454163 9683351 460739 9641901 3.0 1.65275 3109918 53109 3041239 4.0 1.740939 1023935 18990 974138 5.0 1.780102 347340 8152 317256 6.0 1.797494 121574 3969 104669 7.0 1.805217 44016 2028 34553 8.0 1.808647 17427 1092 12002 9.0 1.81017 7128 635 4124 10.0 1.810846 3311 416 1533 11.0 1.811147 1781 240 582 12.0 1.81128 945 170 245 13.0 1.811339 645 89 127 14.0 1.811366 424 78 82 15.0 1.811377 282 41 34 16.0 1.811383 199 39 28 17.0 1.811385 127 31 18 18.0 1.811386 129 24 21 19.0 1.811386 73 19 15 20.0 1.811387 61 14 8 21.0 1.811387 43 6 6 22.0 1.811387 43 12 13 23.0 1.811387 38 4 7 24.0 1.811387 35 7 10 25.0 1.811387 17 8 4 26.0 1.811387 14 3 3 27.0 1.811387 8 3 3 28.0 1.811387 18 1 5 29.0 1.811387 10 2 4 30.0 1.811387 8 2 1 31.0 1.811387 11 2 7 32.0 1.811387 12 1 2 33.0 1.811387 7 2 1 34.0 1.811387 2 1 0 35.0 1.811387 4 3 2 36.0 1.811387 1 1 0 37.0 1.811387 3 0 0 38.0 1.811387 1 0 0 39.0 1.811387 3 2 1 40.0 1.811387 4 0 2 41.0 1.811387 2 0 0 42.0 1.811387 1 0 1 43.0 1.811387 2 0 0 44.0 1.811387 1 1 1 45.0 1.811387 3 0 2 46.0 1.811387 4 0 1 47.0 1.811387 0 1 1 48.0 1.811387 1 0 0 49.0 1.811387 2 0 0 50.0 1.811387 0 0 0 51.0 1.811387 2 0 2 52.0 1.811387 1 0 2 53.0 1.811387 1 0 0 54.0 1.811387 1 0 0 55.0 1.811387 0 0 0 56.0 1.811387 0 0 0 57.0 1.811387 0 0 0 58.0 1.811387 0 0 0 59.0 1.811387 0 0 0 60.0 1.811387 2 0 0 61.0 1.811387 0 0 0 62.0 1.811387 0 0 0 63.0 1.811387 0 0 0 64.0 1.811387 0 0 0 65.0 1.811387 0 0 0 66.0 1.811387 0 0 0 67.0 1.811387 0 0 0 68.0 1.811387 0 0 0 69.0 1.811387 0 0 0 70.0 1.811387 0 0 0 71.0 1.811387 0 0 0 72.0 1.811387 0 0 0 73.0 1.811387 0 0 0 74.0 1.811387 0 0 0 75.0 1.811387 0 0 0 76.0 1.811387 0 0 0 77.0 1.811387 0 0 0 78.0 1.811387 0 0 0 79.0 1.811387 0 0 0 80.0 1.811387 0 0 0 81.0 1.811387 0 0 1 82.0 1.811387 1 0 0 83.0 1.811387 0 0 0 84.0 1.811387 0 0 0 85.0 1.811387 0 0 0 86.0 1.811387 0 0 0 87.0 1.811387 0 0 0 88.0 1.811387 0 0 0 89.0 1.811387 0 0 0 90.0 1.811387 0 0 0 91.0 1.811387 0 0 0 92.0 1.811387 0 0 0 93.0 1.811387 0 0 0 94.0 1.811387 0 0 0 95.0 1.811387 0 0 0 96.0 1.811387 0 0 0 97.0 1.811387 0 0 0 98.0 1.811387 0 0 0 99.0 1.811387 0 0 0 100.0 1.811387 0 0 0