## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/PT_Por_Rec_1_2015-09-01/PT_Por_Rec_1_2015-09-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/PT_Por_Rec_1_2015-09-01/PT_Por_Rec_1_2015-09-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/PT_Por_Rec_1_2015-09-01/PT_Por_Rec_1_2015-09-01.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 09:59:28 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 8626384 38709174 0 0 3267353 3411866 0 0.117277 206484529 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 30745678 30745678 2.0 1.829056 2681341 2681341 3.0 2.51639 218522 218522 4.0 3.086228 22098 22098 5.0 3.558655 5057 5057 6.0 3.950324 2531 2531 7.0 4.27504 1657 1657 8.0 4.544247 1180 1180 9.0 4.767435 929 929 10.0 4.95247 742 742 11.0 5.105875 574 574 12.0 5.233056 471 471 13.0 5.338496 414 414 14.0 5.425911 343 343 15.0 5.498384 271 271 16.0 5.558468 260 260 17.0 5.608281 240 240 18.0 5.649578 216 216 19.0 5.683816 188 188 20.0 5.712202 160 160 21.0 5.735735 149 149 22.0 5.755245 154 154 23.0 5.77142 110 110 24.0 5.78483 122 122 25.0 5.795947 91 91 26.0 5.805164 88 88 27.0 5.812806 81 81 28.0 5.819141 73 73 29.0 5.824393 70 70 30.0 5.828748 49 49 31.0 5.832358 45 45 32.0 5.835351 62 62 33.0 5.837832 53 53 34.0 5.839889 37 37 35.0 5.841595 49 49 36.0 5.843009 48 48 37.0 5.844181 42 42 38.0 5.845153 29 29 39.0 5.845959 32 32 40.0 5.846627 25 25 41.0 5.84718 24 24 42.0 5.847639 29 29 43.0 5.84802 35 35 44.0 5.848336 21 21 45.0 5.848597 18 18 46.0 5.848814 24 24 47.0 5.848994 20 20 48.0 5.849143 19 19 49.0 5.849267 29 29 50.0 5.849369 26 26 51.0 5.849454 14 14 52.0 5.849525 10 10 53.0 5.849583 20 20 54.0 5.849631 16 16 55.0 5.849672 12 12 56.0 5.849705 18 18 57.0 5.849732 19 19 58.0 5.849755 14 14 59.0 5.849774 11 11 60.0 5.84979 20 20 61.0 5.849803 16 16 62.0 5.849814 11 11 63.0 5.849823 14 14 64.0 5.84983 13 13 65.0 5.849836 16 16 66.0 5.849841 10 10 67.0 5.849846 11 11 68.0 5.849849 16 16 69.0 5.849852 13 13 70.0 5.849855 15 15 71.0 5.849857 6 6 72.0 5.849858 11 11 73.0 5.84986 7 7 74.0 5.849861 9 9 75.0 5.849862 11 11 76.0 5.849862 8 8 77.0 5.849863 7 7 78.0 5.849864 9 9 79.0 5.849864 9 9 80.0 5.849864 10 10 81.0 5.849865 5 5 82.0 5.849865 8 8 83.0 5.849865 5 5 84.0 5.849865 11 11 85.0 5.849865 6 6 86.0 5.849866 6 6 87.0 5.849866 7 7 88.0 5.849866 5 5 89.0 5.849866 12 12 90.0 5.849866 4 4 91.0 5.849866 6 6 92.0 5.849866 4 4 93.0 5.849866 1 1 94.0 5.849866 4 4 95.0 5.849866 7 7 96.0 5.849866 7 7 97.0 5.849866 6 6 98.0 5.849866 4 4 99.0 5.849866 4 4 100.0 5.849866 5 5 101.0 0 6 6 102.0 0 8 8 103.0 0 5 5 104.0 0 2 2 105.0 0 2 2 106.0 0 3 3 107.0 0 3 3 108.0 0 5 5 109.0 0 3 3 110.0 0 4 4 111.0 0 1 1 112.0 0 4 4 113.0 0 5 5 114.0 0 5 5 115.0 0 2 2 116.0 0 3 3 117.0 0 3 3 118.0 0 2 2 119.0 0 3 3 120.0 0 2 2 121.0 0 2 2 122.0 0 1 1 123.0 0 4 4 124.0 0 3 3 125.0 0 3 3 126.0 0 1 1 127.0 0 1 1 128.0 0 1 1 129.0 0 1 1 130.0 0 1 1 131.0 0 2 2 132.0 0 1 1 136.0 0 1 1 137.0 0 2 2 138.0 0 2 2 140.0 0 1 1 141.0 0 2 2 142.0 0 2 2 143.0 0 3 3 144.0 0 2 2 146.0 0 2 2 148.0 0 1 1 149.0 0 1 1 151.0 0 1 1 152.0 0 1 1 154.0 0 3 3 157.0 0 1 1 159.0 0 2 2 161.0 0 1 1 162.0 0 1 1 164.0 0 1 1 166.0 0 2 2 167.0 0 3 3 168.0 0 1 1 170.0 0 1 1 171.0 0 2 2 172.0 0 3 3 174.0 0 1 1 175.0 0 2 2 177.0 0 1 1 178.0 0 3 3 179.0 0 2 2 180.0 0 2 2 187.0 0 2 2 188.0 0 3 3 189.0 0 1 1 190.0 0 1 1 191.0 0 1 1 192.0 0 1 1 194.0 0 2 2 195.0 0 1 1 197.0 0 3 3 198.0 0 1 1 200.0 0 2 2 201.0 0 2 2 206.0 0 2 2 208.0 0 1 1 209.0 0 1 1 211.0 0 1 1 213.0 0 1 1 216.0 0 1 1 226.0 0 1 1 228.0 0 1 1 237.0 0 2 2 238.0 0 1 1 239.0 0 2 2 240.0 0 1 1 244.0 0 1 1 248.0 0 1 1 249.0 0 1 1 250.0 0 1 1 251.0 0 1 1 261.0 0 1 1 266.0 0 1 1 275.0 0 1 1 279.0 0 1 1 294.0 0 1 1 305.0 0 1 1 311.0 0 1 1 315.0 0 1 1 319.0 0 1 1 323.0 0 1 1 324.0 0 1 1 327.0 0 1 1 358.0 0 1 1 383.0 0 1 1 400.0 0 1 1 430.0 0 1 1 446.0 0 1 1 584.0 0 1 1 667.0 0 1 1 720.0 0 1 1 761.0 0 1 1 912.0 0 1 1 1232.0 0 1 1