## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_9/ALK_9_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_9/ALK_9_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_9/ALK_9_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 17:00:03 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 118873 47202907 16276982 140937 90315 27436533 540909 0.581471 22654630 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.003447 9341489 0 9400626 2.0 1.128359 4295013 279816 4311018 3.0 1.143909 2352018 47880 2351623 4.0 1.145844 1380851 19418 1373118 5.0 1.146085 845307 9093 834891 6.0 1.146115 531887 4494 521624 7.0 1.146119 341578 2401 331950 8.0 1.14612 222357 1356 214419 9.0 1.14612 146435 833 140017 10.0 1.14612 98282 476 92987 11.0 1.14612 66075 302 62268 12.0 1.14612 44841 209 41703 13.0 1.14612 30672 129 28270 14.0 1.14612 21027 100 19241 15.0 1.14612 14444 70 13041 16.0 1.14612 10104 57 9172 17.0 1.14612 7116 33 6191 18.0 1.14612 4977 34 4388 19.0 1.14612 3442 21 3000 20.0 1.14612 2474 18 2059 21.0 1.14612 1654 10 1372 22.0 1.14612 1270 8 1042 23.0 1.14612 844 7 689 24.0 1.14612 634 8 497 25.0 1.14612 435 7 357 26.0 1.14612 332 3 266 27.0 1.14612 236 2 181 28.0 1.14612 167 1 112 29.0 1.14612 104 3 66 30.0 1.14612 87 4 58 31.0 1.14612 57 0 33 32.0 1.14612 33 3 20 33.0 1.14612 20 1 16 34.0 1.14612 19 2 11 35.0 1.14612 18 0 8 36.0 1.14612 12 0 9 37.0 1.14612 10 0 3 38.0 1.14612 8 0 6 39.0 1.14612 9 0 5 40.0 1.14612 5 0 3 41.0 1.14612 4 0 2 42.0 1.14612 5 0 3 43.0 1.14612 6 0 0 44.0 1.14612 1 0 1 45.0 1.14612 0 0 0 46.0 1.14612 2 0 0 47.0 1.14612 2 0 1 48.0 1.14612 0 0 1 49.0 1.14612 1 0 0 50.0 1.14612 1 1 0 51.0 1.14612 0 0 0 52.0 1.14612 0 0 0 53.0 1.14612 0 0 0 54.0 1.14612 3 0 1 55.0 1.14612 0 0 0 56.0 1.14612 0 0 0 57.0 1.14612 0 0 0 58.0 1.14612 0 0 0 59.0 1.14612 0 0 0 60.0 1.14612 1 0 0 61.0 1.14612 0 0 0 62.0 1.14612 0 0 0 63.0 1.14612 0 0 0 64.0 1.14612 0 0 0 65.0 1.14612 0 0 0 66.0 1.14612 0 0 0 67.0 1.14612 0 0 0 68.0 1.14612 0 0 0 69.0 1.14612 0 0 0 70.0 1.14612 0 0 0 71.0 1.14612 1 0 1 72.0 1.14612 0 0 0 73.0 1.14612 0 0 0 74.0 1.14612 0 0 0 75.0 1.14612 0 0 0 76.0 1.14612 0 0 0 77.0 1.14612 0 0 0 78.0 1.14612 0 0 0 79.0 1.14612 0 0 0 80.0 1.14612 0 0 0 81.0 1.14612 0 0 0 82.0 1.14612 1 0 1 83.0 1.14612 0 0 0 84.0 1.14612 0 0 0 85.0 1.14612 1 0 1 86.0 1.14612 0 0 0 87.0 1.14612 0 0 0 88.0 1.14612 1 0 1 89.0 1.14612 0 0 0 90.0 1.14612 0 0 0 91.0 1.14612 0 0 0 92.0 1.14612 0 0 0 93.0 1.14612 0 0 0 94.0 1.14612 0 0 0 95.0 1.14612 0 0 0 96.0 1.14612 0 1 0 97.0 1.14612 0 0 0 98.0 1.14612 0 0 0 99.0 1.14612 0 0 0 100.0 1.14612 0 0 0 146.0 0 0 0 1 241.0 0 1 0 0