## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/SgC_2/SgC_2_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/SgC_2/SgC_2_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/SgC_2/SgC_2_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 147112 79836797 29003671 179372 116478 46196203 907340 0.578829 38658862 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.00346 15656108 0 15757665 2.0 1.130697 7458180 483714 7487086 3.0 1.14683 4127903 77323 4126269 4.0 1.148876 2414081 31260 2400061 5.0 1.149135 1460807 14396 1441441 6.0 1.149168 901886 7320 884262 7.0 1.149172 568422 3941 551596 8.0 1.149173 363125 2252 348985 9.0 1.149173 233851 1332 222842 10.0 1.149173 152794 768 144135 11.0 1.149173 100328 563 93887 12.0 1.149173 65940 352 60887 13.0 1.149173 44193 238 40476 14.0 1.149173 29563 158 26664 15.0 1.149173 19951 132 17715 16.0 1.149173 13349 105 11656 17.0 1.149173 9177 63 8024 18.0 1.149173 6278 56 5281 19.0 1.149173 4236 39 3536 20.0 1.149173 3004 29 2477 21.0 1.149173 2027 34 1602 22.0 1.149173 1373 14 1083 23.0 1.149173 963 15 761 24.0 1.149173 720 3 519 25.0 1.149173 489 11 366 26.0 1.149173 351 9 263 27.0 1.149173 274 7 188 28.0 1.149173 187 4 128 29.0 1.149173 169 5 108 30.0 1.149173 121 6 73 31.0 1.149173 83 3 55 32.0 1.149173 79 3 45 33.0 1.149173 67 2 40 34.0 1.149173 52 0 32 35.0 1.149173 36 0 30 36.0 1.149173 42 0 24 37.0 1.149173 31 2 30 38.0 1.149173 31 0 23 39.0 1.149173 21 3 19 40.0 1.149173 25 0 13 41.0 1.149173 13 0 13 42.0 1.149173 23 1 18 43.0 1.149173 16 0 11 44.0 1.149173 15 0 11 45.0 1.149173 10 0 8 46.0 1.149173 7 0 9 47.0 1.149173 10 0 9 48.0 1.149173 13 0 11 49.0 1.149173 15 0 10 50.0 1.149173 11 0 9 51.0 1.149173 8 1 9 52.0 1.149173 11 0 11 53.0 1.149173 9 0 8 54.0 1.149173 10 0 7 55.0 1.149173 6 0 7 56.0 1.149173 5 0 4 57.0 1.149173 1 0 0 58.0 1.149173 5 0 5 59.0 1.149173 4 0 4 60.0 1.149173 3 0 5 61.0 1.149173 5 0 7 62.0 1.149173 1 0 2 63.0 1.149173 11 0 5 64.0 1.149173 1 0 1 65.0 1.149173 2 0 3 66.0 1.149173 2 0 1 67.0 1.149173 3 0 4 68.0 1.149173 2 0 4 69.0 1.149173 1 0 2 70.0 1.149173 5 0 3 71.0 1.149173 2 0 2 72.0 1.149173 2 0 2 73.0 1.149173 2 0 1 74.0 1.149173 2 0 4 75.0 1.149173 3 0 1 76.0 1.149173 2 0 4 77.0 1.149173 3 0 2 78.0 1.149173 1 0 0 79.0 1.149173 0 0 0 80.0 1.149173 0 0 1 81.0 1.149173 1 0 0 82.0 1.149173 0 0 0 83.0 1.149173 2 0 3 84.0 1.149173 0 0 0 85.0 1.149173 2 0 2 86.0 1.149173 2 0 1 87.0 1.149173 2 0 1 88.0 1.149173 1 0 1 89.0 1.149173 0 0 0 90.0 1.149173 0 0 0 91.0 1.149173 1 0 1 92.0 1.149173 1 0 3 93.0 1.149173 2 0 2 94.0 1.149173 2 0 2 95.0 1.149173 2 0 1 96.0 1.149173 0 0 0 97.0 1.149173 1 0 0 98.0 1.149173 0 0 0 99.0 1.149173 0 0 0 100.0 1.149173 1 0 2 102.0 0 1 0 2 103.0 0 0 0 2 104.0 0 4 0 0 111.0 0 0 0 1 112.0 0 1 0 0 118.0 0 1 0 1 122.0 0 1 0 1 123.0 0 0 0 1 124.0 0 2 0 0 135.0 0 1 0 1 146.0 0 0 0 1 149.0 0 1 0 0