## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2012-09-13/US_Pen_Lin_1_2012-09-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2012-09-13/US_Pen_Lin_1_2012-09-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2012-09-13/US_Pen_Lin_1_2012-09-13.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 17:47:28 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 3724769 33796384 0 0 1152516 153279 0 0.020459 3714597033 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 33322829 33322829 2.0 1.990943 21242 21242 3.0 2.972911 1469 1469 4.0 3.945985 436 436 5.0 4.910247 243 243 6.0 5.865774 163 163 7.0 6.812648 130 130 8.0 7.750946 89 89 9.0 8.680746 95 95 10.0 9.602124 65 65 11.0 10.515158 55 55 12.0 11.419922 52 52 13.0 12.316492 39 39 14.0 13.204941 44 44 15.0 14.085344 32 32 16.0 14.957773 43 43 17.0 15.822301 33 33 18.0 16.678998 18 18 19.0 17.527936 19 19 20.0 18.369186 16 16 21.0 19.202816 16 16 22.0 20.028896 13 13 23.0 20.847494 14 14 24.0 21.658679 8 8 25.0 22.462516 16 16 26.0 23.259073 10 10 27.0 24.048416 3 3 28.0 24.830609 5 5 29.0 25.605718 4 4 30.0 26.373807 6 6 31.0 27.13494 6 6 32.0 27.889179 5 5 33.0 28.636586 7 7 34.0 29.377225 3 3 35.0 30.111155 2 2 36.0 30.838439 4 4 37.0 31.559135 3 3 38.0 32.273304 4 4 39.0 32.981004 5 5 40.0 33.682295 2 2 41.0 34.377235 2 2 42.0 35.06588 2 2 43.0 35.748289 4 4 44.0 36.424516 6 6 45.0 37.09462 7 7 46.0 37.758654 1 1 47.0 38.416673 5 5 48.0 39.068734 1 1 49.0 39.714888 0 0 50.0 40.35519 6 6 51.0 40.989693 3 3 52.0 41.61845 3 3 53.0 42.241511 1 1 54.0 42.85893 2 2 55.0 43.470757 3 3 56.0 44.077042 0 0 57.0 44.677836 3 3 58.0 45.273189 4 4 59.0 45.86315 4 4 60.0 46.447767 1 1 61.0 47.02709 1 1 62.0 47.601166 2 2 63.0 48.170042 3 3 64.0 48.733766 6 6 65.0 49.292384 1 1 66.0 49.845943 3 3 67.0 50.394488 0 0 68.0 50.938065 3 3 69.0 51.476719 4 4 70.0 52.010495 1 1 71.0 52.539436 0 0 72.0 53.063586 1 1 73.0 53.582989 2 2 74.0 54.097688 3 3 75.0 54.607725 1 1 76.0 55.113143 3 3 77.0 55.613983 3 3 78.0 56.110287 1 1 79.0 56.602097 2 2 80.0 57.089451 1 1 81.0 57.572392 1 1 82.0 58.050959 1 1 83.0 58.525192 0 0 84.0 58.995129 1 1 85.0 59.46081 2 2 86.0 59.922274 0 0 87.0 60.379557 0 0 88.0 60.8327 0 0 89.0 61.281738 0 0 90.0 61.726709 2 2 91.0 62.167651 2 2 92.0 62.604598 0 0 93.0 63.037588 0 0 94.0 63.466657 0 0 95.0 63.891839 1 1 96.0 64.313171 2 2 97.0 64.730687 1 1 98.0 65.144421 2 2 99.0 65.554408 0 0 100.0 65.960682 0 0 102.0 0 3 3 103.0 0 3 3 104.0 0 1 1 106.0 0 1 1 107.0 0 2 2 108.0 0 1 1 109.0 0 1 1 111.0 0 1 1 112.0 0 2 2 113.0 0 2 2 114.0 0 1 1 115.0 0 1 1 116.0 0 1 1 119.0 0 2 2 120.0 0 1 1 121.0 0 2 2 123.0 0 1 1 125.0 0 2 2 127.0 0 2 2 129.0 0 1 1 131.0 0 2 2 133.0 0 1 1 135.0 0 1 1 136.0 0 1 1 137.0 0 2 2 138.0 0 1 1 139.0 0 1 1 141.0 0 3 3 142.0 0 1 1 144.0 0 3 3 149.0 0 1 1 150.0 0 3 3 152.0 0 1 1 153.0 0 1 1 155.0 0 1 1 156.0 0 2 2 161.0 0 2 2 162.0 0 1 1 168.0 0 1 1 178.0 0 2 2 191.0 0 1 1 192.0 0 1 1 194.0 0 1 1 198.0 0 1 1 203.0 0 2 2 205.0 0 1 1 206.0 0 1 1 209.0 0 1 1 212.0 0 1 1 214.0 0 1 1 217.0 0 1 1 224.0 0 1 1 226.0 0 1 1 228.0 0 1 1 232.0 0 1 1 234.0 0 1 1 235.0 0 1 1 243.0 0 1 1 244.0 0 1 1 251.0 0 2 2 262.0 0 1 1 266.0 0 1 1 269.0 0 1 1 287.0 0 1 1 288.0 0 1 1 289.0 0 1 1 296.0 0 1 1 297.0 0 1 1 300.0 0 1 1 301.0 0 1 1 311.0 0 2 2 321.0 0 1 1 328.0 0 1 1 359.0 0 1 1 390.0 0 1 1 405.0 0 1 1 417.0 0 1 1 442.0 0 1 1 466.0 0 1 1 476.0 0 1 1 549.0 0 1 1 575.0 0 1 1 579.0 0 1 1 691.0 0 1 1 723.0 0 1 1 857.0 0 1 1 876.0 0 1 1 888.0 0 1 1 908.0 0 1 1 1079.0 0 1 1 1109.0 0 1 1 1383.0 0 1 1 1512.0 0 1 1 1619.0 0 1 1 1664.0 0 1 1 1698.0 0 1 1 2109.0 0 1 1 2475.0 0 1 1 3047.0 0 1 1 3176.0 0 1 1 6947.0 0 1 1 8750.0 0 1 1 9789.0 0 1 1 10570.0 0 1 1 24480.0 0 1 1