## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2014-10-10/UA_Ode_Ode_1_2014-10-10.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2014-10-10/UA_Ode_Ode_1_2014-10-10.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2014-10-10/UA_Ode_Ode_1_2014-10-10.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 16:59:32 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 8149858 18420206 0 0 1602007 622046 0 0.06326 266556969 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 17043724 17043724 2.0 1.933229 362183 362183 3.0 2.804147 7062 7062 4.0 3.616912 833 833 5.0 4.375409 437 437 6.0 5.08326 332 332 7.0 5.743848 250 250 8.0 6.360328 188 188 9.0 6.935645 168 168 10.0 7.472548 150 150 11.0 7.973602 117 117 12.0 8.4412 113 113 13.0 8.877577 102 102 14.0 9.284816 97 97 15.0 9.664863 86 86 16.0 10.019535 72 72 17.0 10.350525 75 75 18.0 10.659414 63 63 19.0 10.947679 67 67 20.0 11.216697 54 54 21.0 11.467751 52 52 22.0 11.702043 45 45 23.0 11.920691 44 44 24.0 12.12474 41 41 25.0 12.315164 52 52 26.0 12.492873 38 38 27.0 12.658717 43 43 28.0 12.813488 30 30 29.0 12.957924 40 40 30.0 13.092716 31 31 31.0 13.218508 21 21 32.0 13.3359 27 27 33.0 13.445455 31 31 34.0 13.547694 23 23 35.0 13.643107 23 23 36.0 13.732149 21 21 37.0 13.815246 11 11 38.0 13.892794 17 17 39.0 13.965164 19 19 40.0 14.032702 18 18 41.0 14.095731 25 25 42.0 14.154551 16 16 43.0 14.209443 22 22 44.0 14.260671 17 17 45.0 14.308478 15 15 46.0 14.353093 20 20 47.0 14.394728 25 25 48.0 14.433584 11 11 49.0 14.469846 15 15 50.0 14.503686 13 13 51.0 14.535266 10 10 52.0 14.564738 11 11 53.0 14.592243 13 13 54.0 14.61791 7 7 55.0 14.641864 16 16 56.0 14.664219 15 15 57.0 14.68508 12 12 58.0 14.704549 12 12 59.0 14.722718 7 7 60.0 14.739674 9 9 61.0 14.755498 13 13 62.0 14.770265 14 14 63.0 14.784046 7 7 64.0 14.796907 13 13 65.0 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