## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2015-08-10/FR_Ess_Vil_1_2015-08-10.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2015-08-10/FR_Ess_Vil_1_2015-08-10.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2015-08-10/FR_Ess_Vil_1_2015-08-10.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 08:58:29 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 10160523 33104440 0 0 4142217 3179921 0 0.137517 161095072 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 26654648 26654648 2.0 1.814243 2602089 2602089 3.0 2.477235 220816 220816 4.0 3.017072 19400 19400 5.0 3.45663 2658 2658 6.0 3.814537 981 981 7.0 4.10596 586 586 8.0 4.34325 416 416 9.0 4.536461 320 320 10.0 4.693782 240 240 11.0 4.82188 224 224 12.0 4.926183 158 158 13.0 5.01111 162 162 14.0 5.080262 148 148 15.0 5.136568 89 89 16.0 5.182415 104 104 17.0 5.219746 71 71 18.0 5.250142 65 65 19.0 5.274892 67 67 20.0 5.295045 68 68 21.0 5.311454 41 41 22.0 5.324815 40 40 23.0 5.335694 32 32 24.0 5.344552 28 28 25.0 5.351764 17 17 26.0 5.357637 26 26 27.0 5.362419 27 27 28.0 5.366313 28 28 29.0 5.369483 25 25 30.0 5.372065 21 21 31.0 5.374167 20 20 32.0 5.375878 22 22 33.0 5.377272 19 19 34.0 5.378407 16 16 35.0 5.379331 14 14 36.0 5.380083 18 18 37.0 5.380695 12 12 38.0 5.381194 22 22 39.0 5.3816 16 16 40.0 5.381931 12 12 41.0 5.3822 14 14 42.0 5.382419 13 13 43.0 5.382598 16 16 44.0 5.382743 10 10 45.0 5.382862 7 7 46.0 5.382958 5 5 47.0 5.383037 5 5 48.0 5.3831 7 7 49.0 5.383152 11 11 50.0 5.383195 4 4 51.0 5.383229 7 7 52.0 5.383257 11 11 53.0 5.38328 5 5 54.0 5.383299 13 13 55.0 5.383314 7 7 56.0 5.383326 3 3 57.0 5.383336 4 4 58.0 5.383345 4 4 59.0 5.383351 3 3 60.0 5.383357 2 2 61.0 5.383361 2 2 62.0 5.383365 4 4 63.0 5.383368 3 3 64.0 5.38337 1 1 65.0 5.383372 4 4 66.0 5.383374 2 2 67.0 5.383375 1 1 68.0 5.383376 4 4 69.0 5.383377 7 7 70.0 5.383377 4 4 71.0 5.383378 2 2 72.0 5.383378 8 8 73.0 5.383379 1 1 74.0 5.383379 5 5 75.0 5.383379 1 1 76.0 5.38338 6 6 77.0 5.38338 1 1 78.0 5.38338 1 1 79.0 5.38338 6 6 80.0 5.38338 2 2 81.0 5.38338 2 2 82.0 5.38338 4 4 83.0 5.38338 3 3 84.0 5.38338 4 4 85.0 5.38338 2 2 86.0 5.38338 3 3 87.0 5.38338 4 4 88.0 5.38338 4 4 89.0 5.38338 1 1 90.0 5.38338 0 0 91.0 5.38338 2 2 92.0 5.38338 2 2 93.0 5.38338 3 3 94.0 5.38338 3 3 95.0 5.38338 0 0 96.0 5.38338 0 0 97.0 5.38338 2 2 98.0 5.38338 3 3 99.0 5.38338 1 1 100.0 5.38338 2 2 103.0 0 2 2 104.0 0 1 1 106.0 0 1 1 108.0 0 1 1 110.0 0 1 1 111.0 0 1 1 112.0 0 2 2 113.0 0 2 2 114.0 0 1 1 116.0 0 2 2 117.0 0 1 1 118.0 0 1 1 119.0 0 1 1 123.0 0 2 2 125.0 0 1 1 127.0 0 1 1 128.0 0 1 1 130.0 0 1 1 135.0 0 1 1 139.0 0 2 2 148.0 0 1 1 150.0 0 1 1 152.0 0 1 1 153.0 0 1 1 159.0 0 1 1 168.0 0 1 1 169.0 0 1 1 171.0 0 1 1 173.0 0 1 1 179.0 0 1 1 189.0 0 2 2 191.0 0 1 1 194.0 0 1 1 241.0 0 1 1 413.0 0 1 1 467.0 0 1 1 497.0 0 1 1 571.0 0 1 1