## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//UA_Dro_14_27/UA_Dro_14_27.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Dro_14_27/UA_Dro_14_27.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Dro_14_27/UA_Dro_14_27.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: Sun Jun 07 09:34:11 UTC 2020 ## 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 15913983 15855965 0 0 3123796 542880 0 0.088388 226237544 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 14673242 14673242 2.0 1.932314 330113 330113 3.0 2.801524 6809 6809 4.0 3.6119 716 716 5.0 4.367426 443 443 6.0 5.071813 268 268 7.0 5.728523 208 208 8.0 6.340783 166 166 9.0 6.911601 155 155 10.0 7.443783 145 145 11.0 7.939944 113 113 12.0 8.402522 95 95 13.0 8.83379 90 90 14.0 9.235868 80 80 15.0 9.61073 81 81 16.0 9.960219 62 62 17.0 10.286053 68 68 18.0 10.589833 67 67 19.0 10.873051 47 47 20.0 11.137099 55 55 21.0 11.383275 49 49 22.0 11.612788 51 51 23.0 11.826766 36 36 24.0 12.026261 31 31 25.0 12.212253 35 35 26.0 12.385656 35 35 27.0 12.547322 38 38 28.0 12.698046 36 36 29.0 12.838568 25 25 30.0 12.969578 26 26 31.0 13.091721 17 17 32.0 13.205596 25 25 33.0 13.311764 27 27 34.0 13.410746 17 17 35.0 13.503028 18 18 36.0 13.589063 28 28 37.0 13.669276 22 22 38.0 13.744059 19 19 39.0 13.81378 16 16 40.0 13.878783 13 13 41.0 13.939385 21 21 42.0 13.995886 21 21 43.0 14.048562 15 15 44.0 14.097673 17 17 45.0 14.14346 16 16 46.0 14.186147 15 15 47.0 14.225946 13 13 48.0 14.26305 16 16 49.0 14.297643 10 10 50.0 14.329895 13 13 51.0 14.359963 13 13 52.0 14.387997 10 10 53.0 14.414133 13 13 54.0 14.4385 6 6 55.0 14.461217 16 16 56.0 14.482397 10 10 57.0 14.502143 9 9 58.0 14.520553 8 8 59.0 14.537717 7 7 60.0 14.553719 8 8 61.0 14.568638 8 8 62.0 14.582547 6 6 63.0 14.595515 6 6 64.0 14.607604 12 12 65.0 14.618876 4 4 66.0 14.629385 4 4 67.0 14.639182 12 12 68.0 14.648316 7 7 69.0 14.656832 8 8 70.0 14.664772 7 7 71.0 14.672174 9 9 72.0 14.679075 7 7 73.0 14.685509 6 6 74.0 14.691508 7 7 75.0 14.6971 7 7 76.0 14.702314 8 8 77.0 14.707175 7 7 78.0 14.711707 6 6 79.0 14.715933 3 3 80.0 14.719872 4 4 81.0 14.723545 7 7 82.0 14.726969 10 10 83.0 14.730161 8 8 84.0 14.733137 8 8 85.0 14.735912 8 8 86.0 14.738499 5 5 87.0 14.740911 5 5 88.0 14.743159 4 4 89.0 14.745256 9 9 90.0 14.74721 12 12 91.0 14.749033 7 7 92.0 14.750732 8 8 93.0 14.752315 4 4 94.0 14.753792 8 8 95.0 14.755169 6 6 96.0 14.756452 2 2 97.0 14.757649 7 7 98.0 14.758765 2 2 99.0 14.759805 6 6 100.0 14.760775 7 7 101.0 0 5 5 102.0 0 10 10 103.0 0 5 5 104.0 0 3 3 105.0 0 4 4 106.0 0 4 4 107.0 0 1 1 108.0 0 4 4 109.0 0 3 3 110.0 0 3 3 111.0 0 2 2 112.0 0 3 3 113.0 0 3 3 114.0 0 4 4 115.0 0 5 5 116.0 0 3 3 118.0 0 2 2 119.0 0 4 4 120.0 0 4 4 122.0 0 1 1 123.0 0 3 3 124.0 0 3 3 125.0 0 4 4 126.0 0 4 4 127.0 0 3 3 128.0 0 2 2 129.0 0 1 1 130.0 0 2 2 131.0 0 1 1 132.0 0 5 5 133.0 0 5 5 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