## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/69425/69425_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/69425/69425_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/69425/69425_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 93587 38849647 12203210 119347 68351 21575312 444896 0.555565 20362857 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.003864 8600573 0 8655683 2.0 1.152834 3772354 228754 3784474 3.0 1.17494 1982752 40027 1980007 4.0 1.178221 1121542 16370 1112926 5.0 1.178708 664704 7420 654694 6.0 1.17878 405098 3693 396056 7.0 1.178791 254556 1985 246280 8.0 1.178792 161672 1129 155116 9.0 1.178792 104689 604 99400 10.0 1.178793 68082 362 64024 11.0 1.178793 45122 266 42067 12.0 1.178793 30097 145 27646 13.0 1.178793 20226 120 18512 14.0 1.178793 13468 81 12219 15.0 1.178793 9126 57 8111 16.0 1.178793 6333 36 5495 17.0 1.178793 4256 35 3680 18.0 1.178793 2868 27 2473 19.0 1.178793 2068 16 1792 20.0 1.178793 1397 18 1164 21.0 1.178793 1029 7 806 22.0 1.178793 646 6 506 23.0 1.178793 507 12 393 24.0 1.178793 327 5 289 25.0 1.178793 267 4 174 26.0 1.178793 146 3 99 27.0 1.178793 112 3 69 28.0 1.178793 89 2 54 29.0 1.178793 41 2 32 30.0 1.178793 39 1 24 31.0 1.178793 36 0 19 32.0 1.178793 31 1 12 33.0 1.178793 18 0 8 34.0 1.178793 16 0 13 35.0 1.178793 13 0 5 36.0 1.178793 6 0 1 37.0 1.178793 8 0 2 38.0 1.178793 2 1 0 39.0 1.178793 4 0 4 40.0 1.178793 3 0 0 41.0 1.178793 1 1 1 42.0 1.178793 0 0 0 43.0 1.178793 0 0 0 44.0 1.178793 0 0 0 45.0 1.178793 1 0 0 46.0 1.178793 1 0 0 47.0 1.178793 0 0 0 48.0 1.178793 1 0 0 49.0 1.178793 1 0 0 50.0 1.178793 0 0 0 51.0 1.178793 0 0 0 52.0 1.178793 1 0 0 53.0 1.178793 0 0 0 54.0 1.178793 0 0 0 55.0 1.178793 0 1 0 56.0 1.178793 0 0 1 57.0 1.178793 0 0 0 58.0 1.178793 0 0 0 59.0 1.178793 0 0 0 60.0 1.178793 0 0 0 61.0 1.178793 0 0 0 62.0 1.178793 0 0 0 63.0 1.178793 0 0 0 64.0 1.178793 0 0 0 65.0 1.178793 1 0 0 66.0 1.178793 0 0 0 67.0 1.178793 0 0 0 68.0 1.178793 0 0 0 69.0 1.178793 1 0 0 70.0 1.178793 0 0 0 71.0 1.178793 0 0 0 72.0 1.178793 0 0 0 73.0 1.178793 0 0 0 74.0 1.178793 0 0 0 75.0 1.178793 0 0 0 76.0 1.178793 0 0 0 77.0 1.178793 0 0 0 78.0 1.178793 0 0 0 79.0 1.178793 0 0 0 80.0 1.178793 0 0 0 81.0 1.178793 0 0 0 82.0 1.178793 0 0 0 83.0 1.178793 0 0 0 84.0 1.178793 0 0 0 85.0 1.178793 0 0 0 86.0 1.178793 0 0 0 87.0 1.178793 0 0 0 88.0 1.178793 0 0 0 89.0 1.178793 0 0 0 90.0 1.178793 0 0 0 91.0 1.178793 0 0 0 92.0 1.178793 0 0 0 93.0 1.178793 0 0 0 94.0 1.178793 0 0 0 95.0 1.178793 0 0 0 96.0 1.178793 0 0 0 97.0 1.178793 0 0 0 98.0 1.178793 0 0 0 99.0 1.178793 0 0 0 100.0 1.178793 0 0 0 110.0 0 1 0 1 114.0 0 0 0 1 115.0 0 1 0 0 118.0 0 1 0 1 124.0 0 1 0 1