## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Pyr_1_2016-08-23/UA_Che_Pyr_1_2016-08-23.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Pyr_1_2016-08-23/UA_Che_Pyr_1_2016-08-23.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Pyr_1_2016-08-23/UA_Che_Pyr_1_2016-08-23.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 09:32:00 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 41669198 12635463 0 0 12749066 1171862 0 0.225467 63839831 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 10307901 10307901 2.0 1.820432 711888 711888 3.0 2.49354 59819 59819 4.0 3.04578 7610 7610 5.0 3.498855 2528 2528 6.0 3.870572 1502 1502 7.0 4.17554 995 995 8.0 4.425746 721 721 9.0 4.631023 577 577 10.0 4.799439 441 441 11.0 4.937612 372 372 12.0 5.050974 322 322 13.0 5.14398 260 260 14.0 5.220285 219 219 15.0 5.282888 194 194 16.0 5.33425 175 175 17.0 5.376388 139 139 18.0 5.41096 140 140 19.0 5.439324 155 155 20.0 5.462595 102 102 21.0 5.481687 138 138 22.0 5.49735 98 98 23.0 5.510201 96 96 24.0 5.520744 99 99 25.0 5.529395 99 99 26.0 5.536491 107 107 27.0 5.542314 89 89 28.0 5.547091 76 76 29.0 5.55101 78 78 30.0 5.554225 73 73 31.0 5.556863 64 64 32.0 5.559027 70 70 33.0 5.560803 52 52 34.0 5.56226 56 56 35.0 5.563455 55 55 36.0 5.564436 47 47 37.0 5.56524 54 54 38.0 5.5659 48 48 39.0 5.566442 47 47 40.0 5.566886 43 43 41.0 5.567251 36 36 42.0 5.56755 43 43 43.0 5.567795 51 51 44.0 5.567996 34 34 45.0 5.568161 41 41 46.0 5.568297 29 29 47.0 5.568408 40 40 48.0 5.568499 28 28 49.0 5.568574 24 24 50.0 5.568636 23 23 51.0 5.568686 33 33 52.0 5.568727 27 27 53.0 5.568761 41 41 54.0 5.568789 28 28 55.0 5.568812 12 12 56.0 5.56883 18 18 57.0 5.568846 20 20 58.0 5.568858 16 16 59.0 5.568869 25 25 60.0 5.568877 25 25 61.0 5.568884 25 25 62.0 5.56889 11 11 63.0 5.568895 18 18 64.0 5.568898 8 8 65.0 5.568902 16 16 66.0 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