## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_100/LuC_100_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_100/LuC_100_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_100/LuC_100_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 17:00:13 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 143112 80814960 24087995 160412 111914 44909856 829443 0.555912 42281598 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.00345 17112780 0 17217568 2.0 1.151841 8204439 465631 8232413 3.0 1.173785 4436543 70000 4431705 4.0 1.17703 2506923 27651 2489084 5.0 1.17751 1453826 12409 1432305 6.0 1.177581 856994 6169 836965 7.0 1.177591 513590 3128 496957 8.0 1.177593 311481 1636 298325 9.0 1.177593 190892 1045 180582 10.0 1.177593 118138 615 110526 11.0 1.177593 72711 407 67204 12.0 1.177593 45870 238 41669 13.0 1.177593 28850 176 25817 14.0 1.177593 18537 105 16228 15.0 1.177593 11752 78 10098 16.0 1.177593 7280 62 6208 17.0 1.177593 4827 48 4067 18.0 1.177593 3247 28 2594 19.0 1.177593 2028 24 1626 20.0 1.177593 1326 21 1029 21.0 1.177593 863 15 655 22.0 1.177593 650 14 461 23.0 1.177593 394 16 269 24.0 1.177593 273 9 195 25.0 1.177593 209 7 132 26.0 1.177593 140 3 74 27.0 1.177593 91 6 58 28.0 1.177593 75 2 38 29.0 1.177593 55 2 33 30.0 1.177593 51 3 31 31.0 1.177593 39 4 27 32.0 1.177593 34 0 22 33.0 1.177593 24 2 14 34.0 1.177593 16 1 12 35.0 1.177593 15 0 9 36.0 1.177593 19 1 7 37.0 1.177593 15 0 5 38.0 1.177593 9 0 5 39.0 1.177593 7 0 6 40.0 1.177593 8 0 6 41.0 1.177593 5 0 5 42.0 1.177593 8 0 5 43.0 1.177593 6 0 6 44.0 1.177593 5 0 5 45.0 1.177593 2 0 1 46.0 1.177593 8 0 8 47.0 1.177593 3 0 2 48.0 1.177593 3 0 3 49.0 1.177593 4 0 3 50.0 1.177593 1 0 3 51.0 1.177593 2 0 3 52.0 1.177593 4 0 3 53.0 1.177593 5 0 3 54.0 1.177593 1 0 0 55.0 1.177593 2 0 2 56.0 1.177593 2 0 2 57.0 1.177593 2 0 1 58.0 1.177593 0 0 3 59.0 1.177593 5 0 2 60.0 1.177593 0 0 0 61.0 1.177593 0 0 0 62.0 1.177593 0 0 0 63.0 1.177593 0 0 0 64.0 1.177593 1 0 1 65.0 1.177593 0 0 1 66.0 1.177593 0 0 0 67.0 1.177593 1 0 0 68.0 1.177593 1 0 3 69.0 1.177593 2 0 2 70.0 1.177593 2 0 0 71.0 1.177593 0 0 0 72.0 1.177593 0 0 0 73.0 1.177593 0 0 0 74.0 1.177593 0 0 0 75.0 1.177593 0 0 1 76.0 1.177593 2 0 1 77.0 1.177593 0 0 0 78.0 1.177593 0 0 0 79.0 1.177593 0 0 0 80.0 1.177593 0 0 0 81.0 1.177593 0 0 0 82.0 1.177593 0 0 0 83.0 1.177593 1 0 1 84.0 1.177593 0 0 0 85.0 1.177593 0 0 0 86.0 1.177593 0 0 1 87.0 1.177593 1 0 0 88.0 1.177593 2 0 2 89.0 1.177593 0 0 0 90.0 1.177593 0 0 0 91.0 1.177593 0 0 0 92.0 1.177593 0 0 0 93.0 1.177593 0 0 0 94.0 1.177593 0 0 1 95.0 1.177593 1 0 0 96.0 1.177593 0 0 0 97.0 1.177593 0 0 0 98.0 1.177593 0 0 0 99.0 1.177593 0 0 1 100.0 1.177593 0 0 0 101.0 0 1 0 0