## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2016-08-25/ES_Ler_Gim_1_2016-08-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2016-08-25/ES_Ler_Gim_1_2016-08-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2016-08-25/ES_Ler_Gim_1_2016-08-25.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 09:15:26 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 32887610 12310739 0 0 8370100 984087 0 0.179768 72841773 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 10159501 10159501 2.0 1.844503 689224 689224 3.0 2.557689 55844 55844 4.0 3.159977 7707 7707 5.0 3.668611 2767 2767 6.0 4.098154 1577 1577 7.0 4.460905 1129 1129 8.0 4.767249 864 864 9.0 5.025958 718 718 10.0 5.244438 487 487 11.0 5.428946 446 446 12.0 5.584763 343 343 13.0 5.716351 271 271 14.0 5.827477 233 233 15.0 5.921324 224 224 16.0 6.000578 188 188 17.0 6.067508 183 183 18.0 6.124031 113 113 19.0 6.171765 116 116 20.0 6.212076 110 110 21.0 6.246119 93 93 22.0 6.274868 90 90 23.0 6.299147 72 72 24.0 6.319651 71 71 25.0 6.336966 86 86 26.0 6.351589 63 63 27.0 6.363938 73 73 28.0 6.374367 61 61 29.0 6.383175 72 72 30.0 6.390612 60 60 31.0 6.396893 47 47 32.0 6.402198 57 57 33.0 6.406678 53 53 34.0 6.410461 39 39 35.0 6.413655 28 28 36.0 6.416353 36 36 37.0 6.418632 41 41 38.0 6.420556 35 35 39.0 6.422181 30 30 40.0 6.423553 22 22 41.0 6.424712 27 27 42.0 6.425691 25 25 43.0 6.426518 22 22 44.0 6.427216 29 29 45.0 6.427805 19 19 46.0 6.428303 19 19 47.0 6.428723 13 13 48.0 6.429078 16 16 49.0 6.429378 16 16 50.0 6.429631 11 11 51.0 6.429845 11 11 52.0 6.430026 20 20 53.0 6.430178 15 15 54.0 6.430307 14 14 55.0 6.430416 7 7 56.0 6.430508 11 11 57.0 6.430585 13 13 58.0 6.430651 8 8 59.0 6.430706 10 10 60.0 6.430753 4 4 61.0 6.430792 14 14 62.0 6.430826 5 5 63.0 6.430854 11 11 64.0 6.430877 6 6 65.0 6.430898 12 12 66.0 6.430914 6 6 67.0 6.430929 5 5 68.0 6.430941 4 4 69.0 6.430951 8 8 70.0 6.43096 5 5 71.0 6.430967 10 10 72.0 6.430973 1 1 73.0 6.430978 7 7 74.0 6.430983 4 4 75.0 6.430986 5 5 76.0 6.43099 3 3 77.0 6.430992 7 7 78.0 6.430994 4 4 79.0 6.430996 2 2 80.0 6.430998 4 4 81.0 6.430999 3 3 82.0 6.431 1 1 83.0 6.431001 5 5 84.0 6.431002 7 7 85.0 6.431003 4 4 86.0 6.431003 2 2 87.0 6.431004 4 4 88.0 6.431004 3 3 89.0 6.431005 1 1 90.0 6.431005 3 3 91.0 6.431005 3 3 92.0 6.431005 4 4 93.0 6.431006 4 4 94.0 6.431006 6 6 95.0 6.431006 0 0 96.0 6.431006 3 3 97.0 6.431006 1 1 98.0 6.431006 3 3 99.0 6.431006 4 4 100.0 6.431006 3 3 101.0 0 2 2 102.0 0 1 1 103.0 0 1 1 105.0 0 7 7 106.0 0 2 2 107.0 0 3 3 108.0 0 1 1 109.0 0 2 2 110.0 0 5 5 111.0 0 3 3 112.0 0 2 2 113.0 0 1 1 114.0 0 3 3 115.0 0 2 2 116.0 0 2 2 117.0 0 1 1 118.0 0 4 4 119.0 0 5 5 122.0 0 1 1 123.0 0 1 1 124.0 0 1 1 125.0 0 4 4 127.0 0 1 1 128.0 0 3 3 129.0 0 1 1 130.0 0 3 3 131.0 0 1 1 132.0 0 1 1 133.0 0 3 3 134.0 0 1 1 136.0 0 3 3 137.0 0 1 1 139.0 0 3 3 141.0 0 1 1 142.0 0 1 1 143.0 0 3 3 144.0 0 2 2 146.0 0 1 1 147.0 0 1 1 148.0 0 1 1 150.0 0 1 1 151.0 0 2 2 158.0 0 1 1 159.0 0 1 1 166.0 0 1 1 167.0 0 1 1 168.0 0 1 1 175.0 0 1 1 176.0 0 1 1 179.0 0 2 2 182.0 0 1 1 183.0 0 1 1 185.0 0 1 1 186.0 0 1 1 187.0 0 1 1 197.0 0 1 1 198.0 0 1 1 201.0 0 1 1 203.0 0 1 1 209.0 0 2 2 212.0 0 1 1 217.0 0 1 1 218.0 0 1 1 227.0 0 1 1 230.0 0 1 1 241.0 0 1 1 248.0 0 1 1 252.0 0 1 1 263.0 0 2 2 265.0 0 1 1 287.0 0 1 1 313.0 0 1 1 328.0 0 1 1 330.0 0 1 1 339.0 0 1 1 348.0 0 1 1 356.0 0 1 1 357.0 0 1 1 401.0 0 1 1 412.0 0 1 1 421.0 0 1 1 473.0 0 1 1 477.0 0 1 1 485.0 0 1 1 491.0 0 1 1 570.0 0 1 1 575.0 0 1 1 722.0 0 1 1 1006.0 0 1 1 1044.0 0 1 1 2228.0 0 1 1