## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/HU_Sze_Sze_1_2016-08-28/HU_Sze_Sze_1_2016-08-28.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/HU_Sze_Sze_1_2016-08-28/HU_Sze_Sze_1_2016-08-28.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/HU_Sze_Sze_1_2016-08-28/HU_Sze_Sze_1_2016-08-28.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT 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 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 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Jan 20 08:41:01 UTC 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 lib1 23678365 9934246 0 0 4789118 825696 0 0.147898 56401805 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 8243055 8243055 2.0 1.838506 578214 578214 3.0 2.541598 45964 45964 4.0 3.131146 5135 5135 5.0 3.625485 1556 1556 6.0 4.039991 847 847 7.0 4.387557 601 601 8.0 4.678993 442 442 9.0 4.923364 351 351 10.0 5.12827 295 295 11.0 5.300086 229 229 12.0 5.444154 233 233 13.0 5.564956 191 191 14.0 5.666249 197 197 15.0 5.751184 185 185 16.0 5.822403 128 128 17.0 5.88212 125 125 18.0 5.932193 135 135 19.0 5.97418 127 127 20.0 6.009386 111 111 21.0 6.038907 98 98 22.0 6.06366 60 60 23.0 6.084415 79 79 24.0 6.101819 77 77 25.0 6.116412 71 71 26.0 6.128649 49 49 27.0 6.138909 48 48 28.0 6.147512 54 54 29.0 6.154726 49 49 30.0 6.160775 48 48 31.0 6.165847 30 30 32.0 6.1701 22 22 33.0 6.173667 23 23 34.0 6.176657 37 37 35.0 6.179164 16 16 36.0 6.181267 25 25 37.0 6.183029 28 28 38.0 6.184508 25 25 39.0 6.185747 17 17 40.0 6.186786 22 22 41.0 6.187658 27 27 42.0 6.188389 27 27 43.0 6.189001 28 28 44.0 6.189515 23 23 45.0 6.189946 24 24 46.0 6.190307 15 15 47.0 6.19061 17 17 48.0 6.190864 17 17 49.0 6.191077 13 13 50.0 6.191255 26 26 51.0 6.191405 22 22 52.0 6.191531 23 23 53.0 6.191636 17 17 54.0 6.191724 15 15 55.0 6.191798 16 16 56.0 6.19186 14 14 57.0 6.191912 17 17 58.0 6.191956 13 13 59.0 6.191993 16 16 60.0 6.192023 11 11 61.0 6.192049 13 13 62.0 6.192071 9 9 63.0 6.192089 12 12 64.0 6.192104 18 18 65.0 6.192117 16 16 66.0 6.192127 12 12 67.0 6.192136 11 11 68.0 6.192144 19 19 69.0 6.19215 11 11 70.0 6.192155 8 8 71.0 6.19216 11 11 72.0 6.192163 8 8 73.0 6.192166 12 12 74.0 6.192169 12 12 75.0 6.192171 7 7 76.0 6.192173 8 8 77.0 6.192175 9 9 78.0 6.192176 12 12 79.0 6.192177 8 8 80.0 6.192178 9 9 81.0 6.192179 8 8 82.0 6.192179 11 11 83.0 6.19218 5 5 84.0 6.19218 6 6 85.0 6.192181 5 5 86.0 6.192181 6 6 87.0 6.192181 2 2 88.0 6.192181 5 5 89.0 6.192182 6 6 90.0 6.192182 4 4 91.0 6.192182 7 7 92.0 6.192182 3 3 93.0 6.192182 7 7 94.0 6.192182 9 9 95.0 6.192182 4 4 96.0 6.192182 6 6 97.0 6.192182 3 3 98.0 6.192182 3 3 99.0 6.192182 4 4 100.0 6.192182 5 5 101.0 0 4 4 102.0 0 4 4 103.0 0 4 4 106.0 0 2 2 108.0 0 4 4 110.0 0 2 2 111.0 0 1 1 112.0 0 1 1 114.0 0 2 2 116.0 0 5 5 117.0 0 5 5 118.0 0 2 2 120.0 0 1 1 121.0 0 1 1 122.0 0 1 1 123.0 0 2 2 124.0 0 1 1 125.0 0 1 1 127.0 0 2 2 128.0 0 1 1 129.0 0 1 1 130.0 0 2 2 132.0 0 2 2 133.0 0 2 2 134.0 0 3 3 136.0 0 2 2 138.0 0 3 3 140.0 0 1 1 141.0 0 2 2 142.0 0 3 3 143.0 0 1 1 145.0 0 1 1 146.0 0 2 2 147.0 0 1 1 148.0 0 2 2 150.0 0 1 1 151.0 0 2 2 152.0 0 2 2 153.0 0 1 1 154.0 0 1 1 157.0 0 1 1 161.0 0 2 2 162.0 0 2 2 163.0 0 3 3 164.0 0 1 1 166.0 0 1 1 167.0 0 1 1 168.0 0 1 1 169.0 0 1 1 170.0 0 1 1 174.0 0 1 1 175.0 0 2 2 176.0 0 1 1 177.0 0 1 1 179.0 0 1 1 181.0 0 1 1 189.0 0 2 2 191.0 0 2 2 194.0 0 1 1 197.0 0 1 1 199.0 0 2 2 205.0 0 2 2 208.0 0 1 1 214.0 0 1 1 218.0 0 1 1 222.0 0 1 1 224.0 0 2 2 225.0 0 1 1 226.0 0 2 2 231.0 0 1 1 233.0 0 1 1 234.0 0 2 2 243.0 0 1 1 259.0 0 1 1 260.0 0 1 1 273.0 0 1 1 283.0 0 1 1 289.0 0 2 2 296.0 0 1 1 305.0 0 1 1 314.0 0 1 1 329.0 0 1 1 335.0 0 1 1 348.0 0 1 1 354.0 0 1 1 369.0 0 1 1 374.0 0 1 1 440.0 0 1 1 443.0 0 1 1 445.0 0 1 1 495.0 0 1 1 535.0 0 1 1 549.0 0 1 1 585.0 0 1 1 780.0 0 1 1