## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2015-06-24/RU_Cri_Yal_1_2015-06-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2015-06-24/RU_Cri_Yal_1_2015-06-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2015-06-24/RU_Cri_Yal_1_2015-06-24.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 09:17:46 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 5398821 25053763 0 0 2599218 6961036 0 0.297647 36277350 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 11667806 11667806 2.0 1.501267 3523842 3523842 3.0 1.752535 990678 990678 4.0 1.878487 259354 259354 5.0 1.941623 65596 65596 6.0 1.973271 17329 17329 7.0 1.989135 5173 5173 8.0 1.997087 2068 2068 9.0 2.001073 1145 1145 10.0 2.003071 791 791 11.0 2.004072 546 546 12.0 2.004575 479 479 13.0 2.004826 389 389 14.0 2.004952 350 350 15.0 2.005016 280 280 16.0 2.005047 242 242 17.0 2.005063 236 236 18.0 2.005071 192 192 19.0 2.005075 175 175 20.0 2.005077 161 161 21.0 2.005078 154 154 22.0 2.005079 135 135 23.0 2.005079 128 128 24.0 2.005079 109 109 25.0 2.005079 126 126 26.0 2.005079 110 110 27.0 2.005079 105 105 28.0 2.005079 94 94 29.0 2.005079 87 87 30.0 2.005079 86 86 31.0 2.005079 79 79 32.0 2.005079 79 79 33.0 2.005079 59 59 34.0 2.005079 59 59 35.0 2.005079 58 58 36.0 2.005079 57 57 37.0 2.005079 56 56 38.0 2.005079 47 47 39.0 2.005079 46 46 40.0 2.005079 46 46 41.0 2.005079 36 36 42.0 2.005079 48 48 43.0 2.005079 29 29 44.0 2.005079 28 28 45.0 2.005079 36 36 46.0 2.005079 27 27 47.0 2.005079 29 29 48.0 2.005079 41 41 49.0 2.005079 32 32 50.0 2.005079 30 30 51.0 2.005079 28 28 52.0 2.005079 36 36 53.0 2.005079 32 32 54.0 2.005079 16 16 55.0 2.005079 29 29 56.0 2.005079 22 22 57.0 2.005079 25 25 58.0 2.005079 22 22 59.0 2.005079 23 23 60.0 2.005079 24 24 61.0 2.005079 23 23 62.0 2.005079 19 19 63.0 2.005079 15 15 64.0 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