## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Sto_1_2012-10-01/US_Cal_Sto_1_2012-10-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Sto_1_2012-10-01/US_Cal_Sto_1_2012-10-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Sto_1_2012-10-01/US_Cal_Sto_1_2012-10-01.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 17:36:30 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 2691432 32651367 0 0 896475 3155805 0 0.10601 157844031 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 26390950 26390950 2.0 1.813135 2371348 2371348 3.0 2.474323 193507 193507 4.0 3.011958 16509 16509 5.0 3.449128 1974 1974 6.0 3.804606 544 544 7.0 4.093657 289 289 8.0 4.328695 217 217 9.0 4.519812 170 170 10.0 4.675217 126 126 11.0 4.801581 102 102 12.0 4.904333 84 84 13.0 4.987883 66 66 14.0 5.055821 46 46 15.0 5.111064 45 45 16.0 5.155984 51 51 17.0 5.19251 48 48 18.0 5.22221 36 36 19.0 5.246361 41 41 20.0 5.265998 34 34 21.0 5.281966 26 26 22.0 5.29495 25 25 23.0 5.305508 29 29 24.0 5.314093 26 26 25.0 5.321074 32 32 26.0 5.32675 23 23 27.0 5.331366 23 23 28.0 5.335119 21 21 29.0 5.338171 19 19 30.0 5.340652 15 15 31.0 5.34267 12 12 32.0 5.344311 20 20 33.0 5.345645 13 13 34.0 5.34673 13 13 35.0 5.347612 12 12 36.0 5.348329 14 14 37.0 5.348912 17 17 38.0 5.349386 8 8 39.0 5.349772 13 13 40.0 5.350086 9 9 41.0 5.350341 18 18 42.0 5.350548 8 8 43.0 5.350717 12 12 44.0 5.350854 10 10 45.0 5.350965 13 13 46.0 5.351056 4 4 47.0 5.351129 6 6 48.0 5.351189 11 11 49.0 5.351238 4 4 50.0 5.351278 2 2 51.0 5.35131 6 6 52.0 5.351336 4 4 53.0 5.351357 5 5 54.0 5.351375 4 4 55.0 5.351389 8 8 56.0 5.3514 5 5 57.0 5.35141 6 6 58.0 5.351417 2 2 59.0 5.351423 8 8 60.0 5.351428 3 3 61.0 5.351432 1 1 62.0 5.351436 1 1 63.0 5.351438 3 3 64.0 5.351441 5 5 65.0 5.351442 4 4 66.0 5.351444 3 3 67.0 5.351445 3 3 68.0 5.351446 4 4 69.0 5.351447 3 3 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