## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Gua_Sai_1_2015-12-23/FR_Gua_Sai_1_2015-12-23.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Gua_Sai_1_2015-12-23/FR_Gua_Sai_1_2015-12-23.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Gua_Sai_1_2015-12-23/FR_Gua_Sai_1_2015-12-23.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 09:20:44 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 7881239 29895287 0 0 3156698 3790823 0 0.158683 107689226 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 22090421 22090421 2.0 1.757594 2712249 2712249 3.0 2.331544 315506 315506 4.0 2.766365 38368 38368 5.0 3.095783 6554 6554 6.0 3.345348 2215 2215 7.0 3.534417 1363 1363 8.0 3.677655 974 974 9.0 3.786171 797 797 10.0 3.868382 608 608 11.0 3.930665 469 469 12.0 3.97785 423 423 13.0 4.013597 349 349 14.0 4.040679 266 266 15.0 4.061196 249 249 16.0 4.07674 222 222 17.0 4.088515 191 191 18.0 4.097437 174 174 19.0 4.104195 159 159 20.0 4.109316 142 142 21.0 4.113195 99 99 22.0 4.116134 107 107 23.0 4.11836 114 114 24.0 4.120047 121 121 25.0 4.121325 101 101 26.0 4.122293 72 72 27.0 4.123026 92 92 28.0 4.123582 94 94 29.0 4.124003 96 96 30.0 4.124322 91 91 31.0 4.124563 81 81 32.0 4.124746 68 68 33.0 4.124885 68 68 34.0 4.12499 51 51 35.0 4.12507 55 55 36.0 4.12513 63 63 37.0 4.125176 55 55 38.0 4.12521 57 57 39.0 4.125236 67 67 40.0 4.125256 59 59 41.0 4.125271 52 52 42.0 4.125283 62 62 43.0 4.125291 48 48 44.0 4.125298 54 54 45.0 4.125303 49 49 46.0 4.125307 38 38 47.0 4.12531 35 35 48.0 4.125312 31 31 49.0 4.125313 40 40 50.0 4.125315 32 32 51.0 4.125315 28 28 52.0 4.125316 26 26 53.0 4.125317 26 26 54.0 4.125317 34 34 55.0 4.125317 22 22 56.0 4.125318 30 30 57.0 4.125318 20 20 58.0 4.125318 27 27 59.0 4.125318 28 28 60.0 4.125318 25 25 61.0 4.125318 25 25 62.0 4.125318 28 28 63.0 4.125318 23 23 64.0 4.125318 15 15 65.0 4.125318 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