## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2010-11-16/US_Pen_Lin_1_2010-11-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2010-11-16/US_Pen_Lin_1_2010-11-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2010-11-16/US_Pen_Lin_1_2010-11-16.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 18:23:51 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 3097774 46601793 0 0 1294842 289281 0 0.019454 3738113528 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 45782895 45782895 2.0 1.987611 81074 81074 3.0 2.962986 3290 3290 4.0 3.926276 867 867 5.0 4.877633 406 406 6.0 5.817202 261 261 7.0 6.745131 147 147 8.0 7.661564 119 119 9.0 8.566643 84 84 10.0 9.460508 70 70 11.0 10.3433 71 71 12.0 11.215154 43 43 13.0 12.076206 33 33 14.0 12.926591 34 34 15.0 13.76644 28 28 16.0 14.595883 27 27 17.0 15.415051 29 29 18.0 16.22407 27 27 19.0 17.023065 21 21 20.0 17.812162 22 22 21.0 18.591482 18 18 22.0 19.361147 13 13 23.0 20.121277 17 17 24.0 20.871989 13 13 25.0 21.6134 14 14 26.0 22.345625 19 19 27.0 23.068779 13 13 28.0 23.782974 13 13 29.0 24.48832 21 21 30.0 25.184928 8 8 31.0 25.872905 16 16 32.0 26.552358 7 7 33.0 27.223394 12 12 34.0 27.886116 10 10 35.0 28.540627 15 15 36.0 29.187029 14 14 37.0 29.825423 14 14 38.0 30.455908 6 6 39.0 31.078581 11 11 40.0 31.69354 10 10 41.0 32.30088 11 11 42.0 32.900696 6 6 43.0 33.49308 9 9 44.0 34.078125 8 8 45.0 34.655922 7 7 46.0 35.22656 4 4 47.0 35.790129 6 6 48.0 36.346715 4 4 49.0 36.896406 8 8 50.0 37.439286 7 7 51.0 37.97544 9 9 52.0 38.504952 2 2 53.0 39.027904 11 11 54.0 39.544377 8 8 55.0 40.05445 7 7 56.0 40.558205 5 5 57.0 41.055718 3 3 58.0 41.547068 8 8 59.0 42.03233 4 4 60.0 42.51158 7 7 61.0 42.984892 3 3 62.0 43.45234 3 3 63.0 43.913997 2 2 64.0 44.369935 6 6 65.0 44.820224 4 4 66.0 45.264934 3 3 67.0 45.704134 5 5 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