## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2009-07-15/US_Pen_Lin_1_2009-07-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2009-07-15/US_Pen_Lin_1_2009-07-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2009-07-15/US_Pen_Lin_1_2009-07-15.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 21:32:39 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 22076177 113668639 0 0 16382077 1094853 0 0.074462 5862640302 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 110844556 110844556 2.0 1.980798 241916 241916 3.0 2.942763 18419 18419 4.0 3.886256 5489 5489 5.0 4.811633 2870 2870 6.0 5.71924 1660 1660 7.0 6.60942 1096 1096 8.0 7.482507 791 791 9.0 8.338829 640 640 10.0 9.178707 481 481 11.0 10.002459 378 378 12.0 10.810393 264 264 13.0 11.602813 253 253 14.0 12.380017 190 190 15.0 13.142297 164 164 16.0 13.88994 138 138 17.0 14.623227 116 116 18.0 15.342433 113 113 19.0 16.047829 105 105 20.0 16.739681 99 99 21.0 17.418247 92 92 22.0 18.083784 73 73 23.0 18.736541 92 92 24.0 19.376764 55 55 25.0 20.004693 52 52 26.0 20.620566 54 54 27.0 21.224612 59 59 28.0 21.817059 50 50 29.0 22.39813 51 51 30.0 22.968044 40 40 31.0 23.527014 45 45 32.0 24.075251 45 45 33.0 24.61296 31 31 34.0 25.140345 38 38 35.0 25.657603 37 37 36.0 26.164928 37 37 37.0 26.662512 38 38 38.0 27.150541 34 34 39.0 27.6292 35 35 40.0 28.098667 28 28 41.0 28.559119 27 27 42.0 29.01073 33 33 43.0 29.453669 28 28 44.0 29.888103 27 27 45.0 30.314195 18 18 46.0 30.732105 16 16 47.0 31.14199 32 32 48.0 31.544005 20 20 49.0 31.938301 15 15 50.0 32.325025 23 23 51.0 32.704323 19 19 52.0 33.076338 16 16 53.0 33.44121 19 19 54.0 33.799076 19 19 55.0 34.150069 11 11 56.0 34.494323 8 8 57.0 34.831967 10 10 58.0 35.163127 12 12 59.0 35.487929 11 11 60.0 35.806493 10 10 61.0 36.118941 13 13 62.0 36.425389 11 11 63.0 36.725953 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