## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Geo_Ath_1_2014-10-15/US_Geo_Ath_1_2014-10-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Geo_Ath_1_2014-10-15/US_Geo_Ath_1_2014-10-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Geo_Ath_1_2014-10-15/US_Geo_Ath_1_2014-10-15.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 23:35:51 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 5709234 77298943 0 0 3335548 11073516 0 0.158961 243360023 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 54506261 54506261 2.0 1.727871 7703058 7703058 3.0 2.257666 967241 967241 4.0 2.643289 126176 126176 5.0 2.923972 24431 24431 6.0 3.128273 9296 9296 7.0 3.276978 5223 5223 8.0 3.385216 3455 3455 9.0 3.463999 2459 2459 10.0 3.521343 1797 1797 11.0 3.563082 1417 1417 12.0 3.593462 1108 1108 13.0 3.615575 935 935 14.0 3.631671 743 743 15.0 3.643386 593 593 16.0 3.651914 561 561 17.0 3.65812 459 459 18.0 3.662638 383 383 19.0 3.665926 334 334 20.0 3.66832 316 316 21.0 3.670062 289 289 22.0 3.67133 277 277 23.0 3.672253 261 261 24.0 3.672925 240 240 25.0 3.673414 224 224 26.0 3.67377 211 211 27.0 3.674029 171 171 28.0 3.674217 161 161 29.0 3.674355 163 163 30.0 3.674455 169 169 31.0 3.674527 122 122 32.0 3.67458 157 157 33.0 3.674619 122 122 34.0 3.674647 124 124 35.0 3.674667 125 125 36.0 3.674682 109 109 37.0 3.674693 94 94 38.0 3.674701 95 95 39.0 3.674707 109 109 40.0 3.674711 108 108 41.0 3.674714 92 92 42.0 3.674716 80 80 43.0 3.674718 79 79 44.0 3.674719 69 69 45.0 3.67472 70 70 46.0 3.67472 48 48 47.0 3.674721 57 57 48.0 3.674721 52 52 49.0 3.674721 51 51 50.0 3.674721 69 69 51.0 3.674722 54 54 52.0 3.674722 62 62 53.0 3.674722 70 70 54.0 3.674722 50 50 55.0 3.674722 45 45 56.0 3.674722 49 49 57.0 3.674722 47 47 58.0 3.674722 47 47 59.0 3.674722 40 40 60.0 3.674722 44 44 61.0 3.674722 40 40 62.0 3.674722 44 44 63.0 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