## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Sta_1_2015-07-18/US_Pen_Sta_1_2015-07-18.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Sta_1_2015-07-18/US_Pen_Sta_1_2015-07-18.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Sta_1_2015-07-18/US_Pen_Sta_1_2015-07-18.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 20:41:16 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 1651056 49254466 0 0 728143 12209821 0 0.251076 82142006 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 26649279 26649279 2.0 1.549017 7404402 7404402 3.0 1.850437 1677781 1677781 4.0 2.015921 326989 326989 5.0 2.106775 59140 59140 6.0 2.156655 11436 11436 7.0 2.184041 3077 3077 8.0 2.199076 1257 1257 9.0 2.20733 756 756 10.0 2.211862 582 582 11.0 2.21435 455 455 12.0 2.215716 327 327 13.0 2.216466 301 301 14.0 2.216877 258 258 15.0 2.217103 200 200 16.0 2.217228 183 183 17.0 2.217296 165 165 18.0 2.217333 139 139 19.0 2.217354 112 112 20.0 2.217365 106 106 21.0 2.217371 102 102 22.0 2.217375 89 89 23.0 2.217376 77 77 24.0 2.217377 81 81 25.0 2.217378 88 88 26.0 2.217378 77 77 27.0 2.217378 55 55 28.0 2.217379 56 56 29.0 2.217379 50 50 30.0 2.217379 39 39 31.0 2.217379 36 36 32.0 2.217379 50 50 33.0 2.217379 42 42 34.0 2.217379 48 48 35.0 2.217379 23 23 36.0 2.217379 23 23 37.0 2.217379 30 30 38.0 2.217379 25 25 39.0 2.217379 34 34 40.0 2.217379 21 21 41.0 2.217379 27 27 42.0 2.217379 21 21 43.0 2.217379 32 32 44.0 2.217379 24 24 45.0 2.217379 25 25 46.0 2.217379 19 19 47.0 2.217379 25 25 48.0 2.217379 21 21 49.0 2.217379 13 13 50.0 2.217379 12 12 51.0 2.217379 15 15 52.0 2.217379 10 10 53.0 2.217379 18 18 54.0 2.217379 11 11 55.0 2.217379 14 14 56.0 2.217379 16 16 57.0 2.217379 5 5 58.0 2.217379 11 11 59.0 2.217379 16 16 60.0 2.217379 10 10 61.0 2.217379 10 10 62.0 2.217379 15 15 63.0 2.217379 10 10 64.0 2.217379 18 18 65.0 2.217379 4 4 66.0 2.217379 9 9 67.0 2.217379 8 8 68.0 2.217379 6 6 69.0 2.217379 7 7 70.0 2.217379 6 6 71.0 2.217379 6 6 72.0 2.217379 4 4 73.0 2.217379 6 6 74.0 2.217379 4 4 75.0 2.217379 10 10 76.0 2.217379 4 4 77.0 2.217379 4 4 78.0 2.217379 8 8 79.0 2.217379 8 8 80.0 2.217379 4 4 81.0 2.217379 2 2 82.0 2.217379 7 7 83.0 2.217379 3 3 84.0 2.217379 7 7 85.0 2.217379 6 6 86.0 2.217379 6 6 87.0 2.217379 3 3 88.0 2.217379 5 5 89.0 2.217379 4 4 90.0 2.217379 7 7 91.0 2.217379 4 4 92.0 2.217379 6 6 93.0 2.217379 7 7 94.0 2.217379 3 3 95.0 2.217379 3 3 96.0 2.217379 2 2 97.0 2.217379 1 1 98.0 2.217379 5 5 99.0 2.217379 6 6 100.0 2.217379 5 5 101.0 0 1 1 102.0 0 3 3 103.0 0 6 6 104.0 0 4 4 105.0 0 6 6 106.0 0 3 3 107.0 0 2 2 108.0 0 1 1 109.0 0 4 4 110.0 0 3 3 111.0 0 2 2 112.0 0 5 5 113.0 0 5 5 114.0 0 5 5 115.0 0 1 1 116.0 0 3 3 117.0 0 1 1 118.0 0 2 2 120.0 0 3 3 121.0 0 1 1 122.0 0 4 4 123.0 0 1 1 124.0 0 1 1 125.0 0 2 2 126.0 0 1 1 127.0 0 1 1 129.0 0 3 3 130.0 0 1 1 132.0 0 3 3 134.0 0 3 3 135.0 0 1 1 136.0 0 2 2 137.0 0 3 3 138.0 0 2 2 139.0 0 2 2 140.0 0 2 2 141.0 0 3 3 142.0 0 2 2 143.0 0 3 3 144.0 0 2 2 145.0 0 3 3 146.0 0 1 1 147.0 0 3 3 148.0 0 1 1 149.0 0 1 1 151.0 0 1 1 155.0 0 5 5 156.0 0 2 2 157.0 0 2 2 158.0 0 2 2 159.0 0 3 3 160.0 0 1 1 161.0 0 1 1 162.0 0 1 1 163.0 0 2 2 164.0 0 1 1 165.0 0 2 2 166.0 0 2 2 168.0 0 2 2 169.0 0 1 1 170.0 0 2 2 174.0 0 2 2 175.0 0 4 4 176.0 0 2 2 177.0 0 1 1 180.0 0 2 2 181.0 0 3 3 182.0 0 1 1 183.0 0 2 2 184.0 0 1 1 185.0 0 3 3 186.0 0 3 3 187.0 0 1 1 189.0 0 1 1 192.0 0 1 1 193.0 0 1 1 196.0 0 3 3 197.0 0 1 1 198.0 0 1 1 199.0 0 2 2 203.0 0 2 2 204.0 0 1 1 205.0 0 1 1 206.0 0 1 1 207.0 0 1 1 210.0 0 1 1 211.0 0 1 1 212.0 0 2 2 215.0 0 2 2 216.0 0 2 2 218.0 0 1 1 219.0 0 3 3 220.0 0 1 1 221.0 0 2 2 222.0 0 3 3 223.0 0 1 1 225.0 0 1 1 226.0 0 1 1 227.0 0 2 2 230.0 0 1 1 231.0 0 1 1 232.0 0 2 2 234.0 0 1 1 236.0 0 2 2 238.0 0 1 1 240.0 0 1 1 246.0 0 1 1 250.0 0 3 3 252.0 0 1 1 253.0 0 1 1 259.0 0 1 1 262.0 0 1 1 269.0 0 1 1 271.0 0 1 1 273.0 0 1 1 277.0 0 2 2 280.0 0 1 1 292.0 0 1 1 294.0 0 1 1 300.0 0 1 1 302.0 0 2 2 306.0 0 1 1 309.0 0 2 2 324.0 0 2 2 326.0 0 1 1 328.0 0 2 2 342.0 0 1 1 349.0 0 1 1 360.0 0 2 2 364.0 0 1 1 390.0 0 1 1 401.0 0 1 1 420.0 0 1 1