## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT /mnt/workflow/8416784/20240702_213404_FastqsToVCF/call-PreProcessingForVariantDiscovery_GATK4/call-MarkDuplicates/work/_miniwdl_inputs/0/C2L88ACXX_0_3.aligned.unsorted.bam --INPUT /mnt/workflow/8416784/20240702_213404_FastqsToVCF/call-PreProcessingForVariantDiscovery_GATK4/call-MarkDuplicates/work/_miniwdl_inputs/0/C2L88ACXX_0_4.aligned.unsorted.bam --INPUT /mnt/workflow/8416784/20240702_213404_FastqsToVCF/call-PreProcessingForVariantDiscovery_GATK4/call-MarkDuplicates/work/_miniwdl_inputs/0/C2L88ACXX_0_5.aligned.unsorted.bam --OUTPUT PG0001189-BLD.hg38.aligned.unsorted.duplicates_marked.bam --METRICS_FILE PG0001189-BLD.hg38.duplicate_metrics --ASSUME_SORT_ORDER queryname --OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 --VALIDATION_STRINGENCY SILENT --CREATE_MD5_FILE false --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 --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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Thu Jul 04 02:45:10 UTC 2024 ## 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 2188441 650201899 12773304 17333653 580091 6741401 428374 0.010796 33222294991 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000653 638713035 0 639132931 2.0 1.981912 3953216 427371 3538003 3.0 2.944153 417242 417 413432 4.0 3.887746 164768 6 164478 5.0 4.81305 77159 1 76908 6.0 5.720421 39946 1 39853 7.0 6.610207 23235 1 23149 8.0 7.482748 14712 0 14705 9.0 8.338377 10654 0 10660 10.0 9.177424 8181 0 8141 11.0 10.00021 6622 0 6605 12.0 10.807049 5459 0 5471 13.0 11.59825 4580 1 4562 14.0 12.374118 3948 0 3966 15.0 13.134948 3361 0 3342 16.0 13.881033 2806 0 2799 17.0 14.612658 2346 0 2334 18.0 15.330103 1835 0 1830 19.0 16.033643 1532 0 1523 20.0 16.723548 1272 0 1272 21.0 17.400083 1059 0 1057 22.0 18.063505 793 1 771 23.0 18.714069 597 0 600 24.0 19.352025 474 0 466 25.0 19.977617 385 1 386 26.0 20.591084 290 0 283 27.0 21.192661 217 0 212 28.0 21.78258 167 0 168 29.0 22.361065 134 0 135 30.0 22.928338 112 0 109 31.0 23.484618 84 0 79 32.0 24.030116 75 0 73 33.0 24.565041 44 0 42 34.0 25.0896 34 0 35 35.0 25.603991 35 0 36 36.0 26.108414 20 0 16 37.0 26.60306 23 0 22 38.0 27.08812 8 0 8 39.0 27.563778 9 0 8 40.0 28.030218 3 0 5 41.0 28.487618 5 0 4 42.0 28.936153 5 0 5 43.0 29.375995 6 0 5 44.0 29.807312 1 0 1 45.0 30.23027 1 0 1 46.0 30.645031 1 0 1 47.0 31.051753 2 0 2 48.0 31.450592 0 0 0 49.0 31.841702 1 0 1 50.0 32.225231 0 0 0 51.0 32.601328 0 0 0 52.0 32.970135 0 0 0 53.0 33.331794 1 0 1 54.0 33.686444 0 0 0 55.0 34.034221 1 0 1 56.0 34.375257 0 0 0 57.0 34.709684 1 0 0 58.0 35.037629 0 0 0 59.0 35.359219 0 0 0 60.0 35.674575 0 0 0 61.0 35.98382 0 0 0 62.0 36.287071 0 0 0 63.0 36.584445 0 0 0 64.0 36.876055 0 0 0 65.0 37.162014 0 0 0 66.0 37.442431 0 0 0 67.0 37.717413 0 0 0 68.0 37.987065 0 0 0 69.0 38.251492 0 0 0 70.0 38.510793 0 0 0 71.0 38.765069 0 0 0 72.0 39.014417 0 0 0 73.0 39.258932 0 0 0 74.0 39.498709 0 0 0 75.0 39.733838 0 0 0 76.0 39.96441 0 0 0 77.0 40.190514 0 0 1 78.0 40.412235 0 0 0 79.0 40.629659 0 0 0 80.0 40.842869 0 1 0 81.0 41.051947 0 0 0 82.0 41.256973 0 0 0 83.0 41.458026 0 0 0 84.0 41.655181 0 0 0 85.0 41.848516 0 0 0 86.0 42.038104 0 0 0 87.0 42.224017 0 0 0 88.0 42.406327 0 0 0 89.0 42.585104 0 0 0 90.0 42.760416 0 0 0 91.0 42.93233 0 0 0 92.0 43.100912 0 0 0 93.0 43.266227 0 0 0 94.0 43.428338 0 0 0 95.0 43.587307 0 0 0 96.0 43.743196 0 0 0 97.0 43.896063 0 0 0 98.0 44.045967 0 0 0 99.0 44.192966 0 0 0 100.0 44.337116 0 0 0 156.0 0 1 0 0