## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[./pipeline_output_destplus/US_Rho_Pro_5_2014-09-25/US_Rho_Pro_5_2014-09-25.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Rho_Pro_5_2014-09-25/US_Rho_Pro_5_2014-09-25.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Rho_Pro_5_2014-09-25/US_Rho_Pro_5_2014-09-25.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: Sat Jan 14 01:54:52 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 1467484 25862268 0 0 369080 178097 0 0.013635 1869157558 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 25311549 25311549 2.0 1.986259 170282 170282 3.0 2.958966 888 888 4.0 3.918306 133 133 5.0 4.864465 72 72 6.0 5.797622 42 42 7.0 6.717957 33 33 8.0 7.625645 19 19 9.0 8.520861 16 16 10.0 9.403775 17 17 11.0 10.274557 10 10 12.0 11.133374 9 9 13.0 11.98039 5 5 14.0 12.815767 4 4 15.0 13.639665 5 5 16.0 14.452242 5 5 17.0 15.253653 2 2 18.0 16.044052 2 2 19.0 16.82359 2 2 20.0 17.592416 1 1 21.0 18.350678 0 0 22.0 19.098521 1 1 23.0 19.836087 0 0 24.0 20.563519 0 0 25.0 21.280955 0 0 26.0 21.988532 0 0 27.0 22.686387 0 0 28.0 23.374652 2 2 29.0 24.05346 0 0 30.0 24.722941 0 0 31.0 25.383222 0 0 32.0 26.03443 0 0 33.0 26.67669 0 0 34.0 27.310124 1 1 35.0 27.934855 0 0 36.0 28.551001 0 0 37.0 29.15868 1 1 38.0 29.75801 0 0 39.0 30.349103 0 0 40.0 30.932075 0 0 41.0 31.507036 0 0 42.0 32.074097 0 0 43.0 32.633365 0 0 44.0 33.184949 0 0 45.0 33.728953 0 0 46.0 34.265482 1 1 47.0 34.794639 0 0 48.0 35.316524 0 0 49.0 35.831238 1 1 50.0 36.33888 1 1 51.0 36.839546 1 1 52.0 37.333332 1 1 53.0 37.820333 1 1 54.0 38.300643 0 0 55.0 38.774352 0 0 56.0 39.241552 0 0 57.0 39.702332 0 0 58.0 40.156781 0 0 59.0 40.604985 0 0 60.0 41.04703 0 0 61.0 41.483001 0 0 62.0 41.912981 0 0 63.0 42.337053 0 0 64.0 42.755298 0 0 65.0 43.167796 1 1 66.0 43.574625 0 0 67.0 43.975865 0 0 68.0 44.371591 0 0 69.0 44.761879 0 0 70.0 45.146804 0 0 71.0 45.52644 0 0 72.0 45.900859 1 1 73.0 46.270133 0 0 74.0 46.634334 0 0 75.0 46.993529 1 1 76.0 47.347789 0 0 77.0 47.697181 0 0 78.0 48.041772 0 0 79.0 48.381629 0 0 80.0 48.716815 0 0 81.0 49.047395 0 0 82.0 49.373433 0 0 83.0 49.69499 0 0 84.0 50.012129 0 0 85.0 50.324911 0 0 86.0 50.633394 0 0 87.0 50.937638 0 0 88.0 51.237702 0 0 89.0 51.533643 0 0 90.0 51.825517 0 0 91.0 52.11338 0 0 92.0 52.397288 0 0 93.0 52.677295 0 0 94.0 52.953454 0 0 95.0 53.225818 0 0 96.0 53.49444 0 0 97.0 53.759371 0 0 98.0 54.020661 0 0 99.0 54.278361 0 0 100.0 54.53252 0 0 234.0 0 1 1 393.0 0 1 1 496.0 0 1 1 626.0 0 1 1 765.0 0 1 1 797.0 0 1 1