## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uMTA1uM_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uMTA1uM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D12_supernatant_RU1uMTA1uM_3.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/tmp] MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Oct 06 02:45:03 CEST 2023 ## 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 620 21738121 21886644 0 530 3767359 0 0.173316 55238555 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16550091 16550091 2.0 1.67467 975692 975692 3.0 2.129849 186154 186154 4.0 2.436945 80099 80099 5.0 2.644134 44697 44697 6.0 2.783918 28767 28767 7.0 2.878226 19340 19340 8.0 2.941852 14159 14159 9.0 2.984779 10762 10762 10.0 3.013741 8052 8052 11.0 3.03328 6508 6508 12.0 3.046463 5370 5370 13.0 3.055357 4283 4283 14.0 3.061358 3595 3595 15.0 3.065406 3093 3093 16.0 3.068137 2692 2692 17.0 3.06998 2264 2264 18.0 3.071223 1927 1927 19.0 3.072062 1733 1733 20.0 3.072628 1524 1524 21.0 3.07301 1398 1398 22.0 3.073267 1199 1199 23.0 3.073441 1095 1095 24.0 3.073558 937 937 25.0 3.073637 910 910 26.0 3.073691 758 758 27.0 3.073727 778 778 28.0 3.073751 670 670 29.0 3.073768 605 605 30.0 3.073779 563 563 31.0 3.073786 562 562 32.0 3.073791 501 501 33.0 3.073794 437 437 34.0 3.073797 393 393 35.0 3.073798 369 369 36.0 3.073799 423 423 37.0 3.0738 331 331 38.0 3.073801 282 282 39.0 3.073801 308 308 40.0 3.073801 273 273 41.0 3.073801 255 255 42.0 3.073801 276 276 43.0 3.073801 236 236 44.0 3.073801 191 191 45.0 3.073801 198 198 46.0 3.073801 164 164 47.0 3.073801 192 192 48.0 3.073801 182 182 49.0 3.073801 159 159 50.0 3.073801 152 152 51.0 3.073801 156 156 52.0 3.073801 165 165 53.0 3.073801 129 129 54.0 3.073801 142 142 55.0 3.073801 108 108 56.0 3.073801 122 122 57.0 3.073801 120 120 58.0 3.073801 119 119 59.0 3.073801 106 106 60.0 3.073801 102 102 61.0 3.073801 89 89 62.0 3.073801 88 88 63.0 3.073801 87 87 64.0 3.073801 92 92 65.0 3.073801 86 86 66.0 3.073801 69 69 67.0 3.073801 68 68 68.0 3.073801 75 75 69.0 3.073801 78 78 70.0 3.073801 69 69 71.0 3.073801 55 55 72.0 3.073801 73 73 73.0 3.073801 61 61 74.0 3.073801 58 58 75.0 3.073801 59 59 76.0 3.073801 56 56 77.0 3.073801 59 59 78.0 3.073801 46 46 79.0 3.073801 37 37 80.0 3.073801 44 44 81.0 3.073801 46 46 82.0 3.073801 42 42 83.0 3.073801 55 55 84.0 3.073801 51 51 85.0 3.073801 52 52 86.0 3.073801 33 33 87.0 3.073801 41 41 88.0 3.073801 47 47 89.0 3.073801 29 29 90.0 3.073801 33 33 91.0 3.073801 32 32 92.0 3.073801 36 36 93.0 3.073801 30 30 94.0 3.073801 30 30 95.0 3.073801 33 33 96.0 3.073801 39 39 97.0 3.073801 27 27 98.0 3.073801 33 33 99.0 3.073801 37 37 100.0 3.073801 24 24 101.0 0 27 27 102.0 0 21 21 103.0 0 27 27 104.0 0 20 20 105.0 0 14 14 106.0 0 27 27 107.0 0 17 17 108.0 0 18 18 109.0 0 20 20 110.0 0 21 21 111.0 0 25 25 112.0 0 25 25 113.0 0 19 19 114.0 0 15 15 115.0 0 17 17 116.0 0 22 22 117.0 0 18 18 118.0 0 20 20 119.0 0 18 18 120.0 0 24 24 121.0 0 23 23 122.0 0 9 9 123.0 0 21 21 124.0 0 24 24 125.0 0 16 16 126.0 0 16 16 127.0 0 19 19 128.0 0 20 20 129.0 0 9 9 130.0 0 7 7 131.0 0 12 12 132.0 0 14 14 133.0 0 13 13 134.0 0 14 14 135.0 0 20 20 136.0 0 13 13 137.0 0 21 21 138.0 0 21 21 139.0 0 11 11 140.0 0 12 12 141.0 0 11 11 142.0 0 8 8 143.0 0 12 12 144.0 0 13 13 145.0 0 12 12 146.0 0 10 10 147.0 0 16 16 148.0 0 10 10 149.0 0 8 8 150.0 0 10 10 151.0 0 10 10 152.0 0 10 10 153.0 0 11 11 154.0 0 13 13 155.0 0 8 8 156.0 0 8 8 157.0 0 11 11 158.0 0 10 10 159.0 0 12 12 160.0 0 8 8 161.0 0 14 14 162.0 0 8 8 163.0 0 9 9 164.0 0 10 10 165.0 0 7 7 166.0 0 9 9 167.0 0 16 16 168.0 0 5 5 169.0 0 6 6 170.0 0 10 10 171.0 0 9 9 172.0 0 3 3 173.0 0 6 6 174.0 0 3 3 175.0 0 9 9 176.0 0 11 11 177.0 0 9 9 178.0 0 4 4 179.0 0 5 5 180.0 0 3 3 181.0 0 6 6 182.0 0 5 5 183.0 0 10 10 184.0 0 8 8 185.0 0 6 6 186.0 0 10 10 187.0 0 8 8 188.0 0 4 4 189.0 0 12 12 190.0 0 7 7 191.0 0 8 8 192.0 0 7 7 193.0 0 6 6 194.0 0 2 2 195.0 0 2 2 196.0 0 3 3 197.0 0 3 3 198.0 0 8 8 199.0 0 1 1 200.0 0 8 8 201.0 0 7 7 202.0 0 4 4 203.0 0 8 8 204.0 0 5 5 205.0 0 7 7 206.0 0 9 9 207.0 0 2 2 208.0 0 3 3 209.0 0 10 10 210.0 0 2 2 211.0 0 2 2 212.0 0 9 9 213.0 0 9 9 214.0 0 4 4 215.0 0 5 5 216.0 0 3 3 217.0 0 4 4 218.0 0 3 3 219.0 0 5 5 220.0 0 2 2 221.0 0 5 5 222.0 0 9 9 223.0 0 3 3 224.0 0 2 2 225.0 0 7 7 226.0 0 4 4 227.0 0 3 3 228.0 0 2 2 229.0 0 4 4 230.0 0 4 4 231.0 0 2 2 232.0 0 1 1 233.0 0 3 3 234.0 0 3 3 235.0 0 6 6 236.0 0 3 3 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