## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_2_2015-08-26/UA_Kie_Cho_2_2015-08-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_2_2015-08-26/UA_Kie_Cho_2_2015-08-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_2_2015-08-26/UA_Kie_Cho_2_2015-08-26.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 15:19:04 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 29964425 14644733 0 0 8362473 1200180 0 0.181639 84397011 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 12183451 12183451 2.0 1.840699 825225 825225 3.0 2.547473 62077 62077 4.0 3.141657 6939 6939 5.0 3.641187 2308 2308 6.0 4.061141 1337 1337 7.0 4.414196 913 913 8.0 4.711009 666 666 9.0 4.960539 518 518 10.0 5.170319 408 408 11.0 5.34668 327 327 12.0 5.494947 270 270 13.0 5.619595 227 227 14.0 5.724386 210 210 15.0 5.812484 188 188 16.0 5.886548 171 171 17.0 5.948813 151 151 18.0 6.00116 131 131 19.0 6.045167 137 137 20.0 6.082164 120 120 21.0 6.113268 92 92 22.0 6.139416 106 106 23.0 6.161399 98 98 24.0 6.17988 95 95 25.0 6.195417 91 91 26.0 6.208479 82 82 27.0 6.219461 66 66 28.0 6.228692 70 70 29.0 6.236454 72 72 30.0 6.242979 79 79 31.0 6.248464 66 66 32.0 6.253076 75 75 33.0 6.256953 52 52 34.0 6.260212 48 48 35.0 6.262952 38 38 36.0 6.265256 51 51 37.0 6.267192 42 42 38.0 6.268821 34 34 39.0 6.270189 49 49 40.0 6.27134 47 47 41.0 6.272307 32 32 42.0 6.273121 35 35 43.0 6.273805 25 25 44.0 6.274379 40 40 45.0 6.274863 25 25 46.0 6.275269 26 26 47.0 6.27561 24 24 48.0 6.275898 23 23 49.0 6.276139 25 25 50.0 6.276342 25 25 51.0 6.276513 24 24 52.0 6.276656 13 13 53.0 6.276777 21 21 54.0 6.276878 21 21 55.0 6.276963 18 18 56.0 6.277035 17 17 57.0 6.277095 23 23 58.0 6.277146 20 20 59.0 6.277188 16 16 60.0 6.277224 21 21 61.0 6.277254 12 12 62.0 6.277279 16 16 63.0 6.277301 13 13 64.0 6.277319 14 14 65.0 6.277334 15 15 66.0 6.277346 12 12 67.0 6.277357 12 12 68.0 6.277366 14 14 69.0 6.277373 14 14 70.0 6.27738 8 8 71.0 6.277385 15 15 72.0 6.277389 13 13 73.0 6.277393 19 19 74.0 6.277396 19 19 75.0 6.277399 12 12 76.0 6.277401 8 8 77.0 6.277403 7 7 78.0 6.277405 10 10 79.0 6.277406 7 7 80.0 6.277407 9 9 81.0 6.277408 17 17 82.0 6.277409 16 16 83.0 6.277409 9 9 84.0 6.27741 12 12 85.0 6.27741 10 10 86.0 6.277411 7 7 87.0 6.277411 11 11 88.0 6.277411 7 7 89.0 6.277412 10 10 90.0 6.277412 12 12 91.0 6.277412 7 7 92.0 6.277412 8 8 93.0 6.277412 5 5 94.0 6.277412 6 6 95.0 6.277413 13 13 96.0 6.277413 8 8 97.0 6.277413 10 10 98.0 6.277413 5 5 99.0 6.277413 5 5 100.0 6.277413 12 12 101.0 0 6 6 102.0 0 7 7 103.0 0 4 4 104.0 0 3 3 105.0 0 7 7 106.0 0 11 11 107.0 0 13 13 108.0 0 4 4 109.0 0 3 3 110.0 0 5 5 111.0 0 4 4 112.0 0 8 8 113.0 0 2 2 114.0 0 4 4 115.0 0 5 5 116.0 0 7 7 117.0 0 8 8 118.0 0 5 5 119.0 0 3 3 120.0 0 2 2 121.0 0 5 5 122.0 0 2 2 123.0 0 2 2 124.0 0 5 5 125.0 0 5 5 126.0 0 6 6 127.0 0 6 6 128.0 0 4 4 129.0 0 4 4 131.0 0 2 2 132.0 0 4 4 133.0 0 4 4 134.0 0 4 4 135.0 0 2 2 136.0 0 1 1 137.0 0 3 3 138.0 0 3 3 139.0 0 3 3 140.0 0 5 5 141.0 0 1 1 142.0 0 3 3 144.0 0 2 2 145.0 0 1 1 146.0 0 1 1 147.0 0 2 2 148.0 0 4 4 149.0 0 1 1 150.0 0 3 3 151.0 0 4 4 152.0 0 2 2 153.0 0 5 5 154.0 0 1 1 155.0 0 2 2 157.0 0 2 2 158.0 0 3 3 159.0 0 2 2 160.0 0 2 2 161.0 0 4 4 162.0 0 4 4 163.0 0 3 3 164.0 0 2 2 165.0 0 3 3 166.0 0 2 2 167.0 0 1 1 168.0 0 5 5 170.0 0 2 2 171.0 0 2 2 172.0 0 2 2 173.0 0 1 1 174.0 0 3 3 175.0 0 1 1 177.0 0 2 2 178.0 0 1 1 179.0 0 2 2 180.0 0 1 1 181.0 0 2 2 182.0 0 3 3 183.0 0 1 1 186.0 0 1 1 187.0 0 1 1 188.0 0 1 1 189.0 0 3 3 192.0 0 3 3 193.0 0 2 2 194.0 0 1 1 195.0 0 1 1 196.0 0 3 3 197.0 0 1 1 199.0 0 1 1 202.0 0 1 1 204.0 0 1 1 206.0 0 1 1 207.0 0 1 1 210.0 0 2 2 213.0 0 2 2 217.0 0 2 2 223.0 0 1 1 225.0 0 1 1 226.0 0 2 2 230.0 0 2 2 236.0 0 1 1 238.0 0 2 2 240.0 0 2 2 241.0 0 1 1 242.0 0 2 2 244.0 0 2 2 245.0 0 2 2 248.0 0 1 1 249.0 0 2 2 250.0 0 1 1 253.0 0 2 2 254.0 0 2 2 255.0 0 2 2 259.0 0 1 1 262.0 0 1 1 269.0 0 1 1 276.0 0 1 1 279.0 0 1 1 281.0 0 2 2 282.0 0 1 1 284.0 0 2 2 288.0 0 1 1 290.0 0 1 1 292.0 0 1 1 298.0 0 1 1 300.0 0 1 1 301.0 0 2 2 311.0 0 2 2 312.0 0 1 1 320.0 0 1 1 322.0 0 1 1 323.0 0 1 1 327.0 0 1 1 330.0 0 1 1 331.0 0 1 1 333.0 0 1 1 337.0 0 1 1 338.0 0 1 1 341.0 0 1 1 348.0 0 1 1 357.0 0 3 3 362.0 0 1 1 363.0 0 1 1 364.0 0 2 2 366.0 0 1 1 369.0 0 1 1 376.0 0 1 1 378.0 0 1 1 381.0 0 2 2 388.0 0 1 1 392.0 0 1 1 412.0 0 1 1 416.0 0 1 1 427.0 0 1 1 433.0 0 1 1 434.0 0 2 2 438.0 0 1 1 442.0 0 1 1 444.0 0 1 1 447.0 0 1 1 455.0 0 1 1 479.0 0 1 1 558.0 0 1 1 571.0 0 1 1 582.0 0 1 1 615.0 0 1 1 620.0 0 1 1 680.0 0 1 1 689.0 0 1 1 1067.0 0 1 1 2288.0 0 1 1