## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2016-08-20/UA_Ode_Ode_1_2016-08-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2016-08-20/UA_Ode_Ode_1_2016-08-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2016-08-20/UA_Ode_Ode_1_2016-08-20.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 17:49:14 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 36544715 5284655 0 0 6958829 337428 0 0.162026 39602054 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 4583515 4583515 2.0 1.875077 215059 215059 3.0 2.640835 15905 15905 4.0 3.310933 2575 2575 5.0 3.89732 968 968 6.0 4.410453 672 672 7.0 4.859484 436 436 8.0 5.25242 375 375 9.0 5.596269 300 300 10.0 5.897164 227 227 11.0 6.16047 217 217 12.0 6.390882 186 186 13.0 6.592511 152 152 14.0 6.768951 142 142 15.0 6.92335 126 126 16.0 7.058461 95 95 17.0 7.176693 99 99 18.0 7.280156 68 68 19.0 7.370693 75 75 20.0 7.449921 80 80 21.0 7.51925 53 53 22.0 7.579919 54 54 23.0 7.633009 53 53 24.0 7.679467 45 45 25.0 7.720121 37 37 26.0 7.755697 33 33 27.0 7.786828 34 34 28.0 7.81407 36 36 29.0 7.837909 26 26 30.0 7.85877 23 23 31.0 7.877025 20 20 32.0 7.893 30 30 33.0 7.906979 21 21 34.0 7.919211 26 26 35.0 7.929916 14 14 36.0 7.939283 14 14 37.0 7.94748 18 18 38.0 7.954653 14 14 39.0 7.96093 15 15 40.0 7.966423 20 20 41.0 7.971229 7 7 42.0 7.975436 19 19 43.0 7.979116 12 12 44.0 7.982337 15 15 45.0 7.985156 10 10 46.0 7.987622 13 13 47.0 7.98978 9 9 48.0 7.991669 11 11 49.0 7.993322 17 17 50.0 7.994768 15 15 51.0 7.996034 9 9 52.0 7.997141 8 8 53.0 7.99811 4 4 54.0 7.998959 9 9 55.0 7.999701 8 8 56.0 8.00035 8 8 57.0 8.000918 4 4 58.0 8.001416 5 5 59.0 8.001851 8 8 60.0 8.002232 10 10 61.0 8.002565 5 5 62.0 8.002857 5 5 63.0 8.003112 4 4 64.0 8.003335 11 11 65.0 8.00353 1 1 66.0 8.003701 5 5 67.0 8.003851 5 5 68.0 8.003982 1 1 69.0 8.004097 1 1 70.0 8.004197 5 5 71.0 8.004285 4 4 72.0 8.004361 3 3 73.0 8.004429 5 5 74.0 8.004487 4 4 75.0 8.004539 5 5 76.0 8.004584 5 5 77.0 8.004623 5 5 78.0 8.004658 2 2 79.0 8.004688 2 2 80.0 8.004714 0 0 81.0 8.004737 0 0 82.0 8.004758 5 5 83.0 8.004775 1 1 84.0 8.004791 3 3 85.0 8.004804 3 3 86.0 8.004816 1 1 87.0 8.004827 1 1 88.0 8.004836 0 0 89.0 8.004844 1 1 90.0 8.004851 3 3 91.0 8.004857 0 0 92.0 8.004862 1 1 93.0 8.004867 2 2 94.0 8.004871 1 1 95.0 8.004874 2 2 96.0 8.004877 2 2 97.0 8.00488 0 0 98.0 8.004883 1 1 99.0 8.004885 1 1 100.0 8.004886 2 2 102.0 0 1 1 103.0 0 3 3 105.0 0 1 1 106.0 0 2 2 108.0 0 2 2 110.0 0 1 1 114.0 0 1 1 115.0 0 2 2 117.0 0 3 3 121.0 0 1 1 122.0 0 1 1 124.0 0 1 1 128.0 0 3 3 129.0 0 1 1 130.0 0 1 1 132.0 0 1 1 133.0 0 1 1 139.0 0 2 2 141.0 0 1 1 142.0 0 2 2 143.0 0 1 1 148.0 0 2 2 154.0 0 1 1 155.0 0 1 1 157.0 0 1 1 173.0 0 2 2 178.0 0 1 1 182.0 0 1 1 187.0 0 1 1 193.0 0 1 1 199.0 0 1 1 203.0 0 1 1 210.0 0 1 1 212.0 0 1 1 213.0 0 2 2 214.0 0 1 1 222.0 0 1 1 227.0 0 1 1 229.0 0 1 1 231.0 0 1 1 232.0 0 1 1 236.0 0 1 1 238.0 0 1 1 239.0 0 1 1 245.0 0 1 1 248.0 0 1 1 250.0 0 1 1 260.0 0 1 1 261.0 0 1 1 284.0 0 1 1 329.0 0 1 1 358.0 0 1 1 395.0 0 1 1 478.0 0 1 1 483.0 0 1 1 523.0 0 1 1 614.0 0 1 1 624.0 0 1 1 1346.0 0 1 1