## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_54/LuC_54_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_54/LuC_54_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_54/LuC_54_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 17:00:15 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 186498 83377534 29094641 210446 142093 40466776 867563 0.485653 55410319 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.004525 23354788 0 23496994 2.0 1.227608 9810599 477454 9833229 3.0 1.277149 4680490 72637 4662437 4.0 1.288151 2362177 29348 2331463 5.0 1.290595 1228394 13704 1199078 6.0 1.291137 655819 6813 631446 7.0 1.291258 357919 3505 339833 8.0 1.291284 197291 1919 184159 9.0 1.29129 111291 1151 101455 10.0 1.291292 62885 711 56426 11.0 1.291292 36431 431 31884 12.0 1.291292 20885 274 17904 13.0 1.291292 12485 180 10231 14.0 1.291292 7173 149 5752 15.0 1.291292 4400 108 3363 16.0 1.291292 2745 78 1982 17.0 1.291292 1708 48 1241 18.0 1.291292 1076 43 715 19.0 1.291292 654 22 427 20.0 1.291292 456 15 262 21.0 1.291292 316 19 169 22.0 1.291292 222 8 96 23.0 1.291292 144 7 67 24.0 1.291292 90 8 34 25.0 1.291292 74 7 25 26.0 1.291292 43 3 20 27.0 1.291292 40 2 10 28.0 1.291292 35 7 12 29.0 1.291292 26 1 10 30.0 1.291292 18 1 6 31.0 1.291292 11 0 2 32.0 1.291292 16 0 7 33.0 1.291292 13 2 2 34.0 1.291292 4 2 1 35.0 1.291292 5 0 2 36.0 1.291292 9 0 3 37.0 1.291292 6 0 2 38.0 1.291292 4 0 3 39.0 1.291292 3 0 0 40.0 1.291292 2 0 2 41.0 1.291292 3 0 1 42.0 1.291292 0 0 0 43.0 1.291292 1 0 0 44.0 1.291292 2 0 1 45.0 1.291292 0 0 0 46.0 1.291292 2 0 1 47.0 1.291292 0 0 0 48.0 1.291292 0 0 0 49.0 1.291292 0 0 0 50.0 1.291292 3 0 1 51.0 1.291292 0 0 0 52.0 1.291292 0 0 0 53.0 1.291292 0 0 0 54.0 1.291292 0 0 0 55.0 1.291292 0 0 0 56.0 1.291292 0 0 0 57.0 1.291292 0 0 0 58.0 1.291292 0 0 0 59.0 1.291292 0 0 0 60.0 1.291292 0 0 0 61.0 1.291292 0 0 0 62.0 1.291292 0 0 0 63.0 1.291292 0 0 0 64.0 1.291292 0 0 0 65.0 1.291292 0 0 0 66.0 1.291292 0 0 0 67.0 1.291292 0 0 0 68.0 1.291292 0 0 0 69.0 1.291292 0 0 0 70.0 1.291292 0 0 0 71.0 1.291292 0 0 0 72.0 1.291292 0 0 0 73.0 1.291292 0 0 0 74.0 1.291292 0 0 0 75.0 1.291292 0 0 0 76.0 1.291292 0 0 0 77.0 1.291292 0 0 0 78.0 1.291292 0 0 0 79.0 1.291292 0 0 0 80.0 1.291292 0 0 0 81.0 1.291292 0 0 0 82.0 1.291292 0 0 0 83.0 1.291292 0 0 0 84.0 1.291292 0 0 0 85.0 1.291292 0 0 0 86.0 1.291292 0 0 0 87.0 1.291292 0 0 0 88.0 1.291292 0 0 0 89.0 1.291292 0 0 0 90.0 1.291292 0 0 0 91.0 1.291292 0 0 0 92.0 1.291292 0 0 0 93.0 1.291292 0 0 0 94.0 1.291292 0 0 0 95.0 1.291292 0 0 0 96.0 1.291292 0 0 0 97.0 1.291292 0 0 0 98.0 1.291292 0 0 0 99.0 1.291292 0 0 0 100.0 1.291292 0 0 0