## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2011-11-16/US_Pen_Lin_1_2011-11-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2011-11-16/US_Pen_Lin_1_2011-11-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2011-11-16/US_Pen_Lin_1_2011-11-16.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 17:40:09 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 49684 39998730 0 0 17193 117637 0 0.003154 6786810164 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 39453201 39453201 2.0 1.994124 102273 102273 3.0 2.982406 4212 4212 4.0 3.96488 339 339 5.0 4.941582 104 104 6.0 5.912544 33 33 7.0 6.8778 27 27 8.0 7.837384 15 15 9.0 8.79133 13 13 10.0 9.739669 11 11 11.0 10.682437 8 8 12.0 11.619664 11 11 13.0 12.551384 7 7 14.0 13.477628 7 7 15.0 14.39843 4 4 16.0 15.313821 7 7 17.0 16.223833 4 4 18.0 17.128498 2 2 19.0 18.027846 2 2 20.0 18.92191 2 2 21.0 19.810719 3 3 22.0 20.694306 3 3 23.0 21.572701 0 0 24.0 22.445934 2 2 25.0 23.314036 2 2 26.0 24.177037 5 5 27.0 25.034966 0 0 28.0 25.887854 1 1 29.0 26.73573 2 2 30.0 27.578624 1 1 31.0 28.416564 0 0 32.0 29.249581 3 3 33.0 30.077703 0 0 34.0 30.900958 2 2 35.0 31.719376 1 1 36.0 32.532985 1 1 37.0 33.341812 1 1 38.0 34.145887 0 0 39.0 34.945237 0 0 40.0 35.739889 0 0 41.0 36.529872 1 1 42.0 37.315213 2 2 43.0 38.095939 0 0 44.0 38.872077 0 0 45.0 39.643654 0 0 46.0 40.410698 0 0 47.0 41.173234 1 1 48.0 41.931289 2 2 49.0 42.68489 0 0 50.0 43.434062 0 0 51.0 44.178832 1 1 52.0 44.919225 0 0 53.0 45.655268 0 0 54.0 46.386986 0 0 55.0 47.114404 1 1 56.0 47.837547 0 0 57.0 48.556441 0 0 58.0 49.27111 0 0 59.0 49.98158 1 1 60.0 50.687875 0 0 61.0 51.39002 0 0 62.0 52.088038 0 0 63.0 52.781955 0 0 64.0 53.471795 0 0 65.0 54.15758 0 0 66.0 54.839336 1 1 67.0 55.517085 0 0 68.0 56.190852 0 0 69.0 56.86066 1 1 70.0 57.526532 0 0 71.0 58.188491 0 0 72.0 58.84656 0 0 73.0 59.500762 0 0 74.0 60.151119 0 0 75.0 60.797656 0 0 76.0 61.440392 0 0 77.0 62.079352 1 1 78.0 62.714558 0 0 79.0 63.34603 0 0 80.0 63.973792 0 0 81.0 64.597865 1 1 82.0 65.218271 0 0 83.0 65.835031 1 1 84.0 66.448167 1 1 85.0 67.0577 0 0 86.0 67.663652 1 1 87.0 68.266042 0 0 88.0 68.864893 0 0 89.0 69.460224 0 0 90.0 70.052058 0 0 91.0 70.640413 1 1 92.0 71.225311 0 0 93.0 71.806773 0 0 94.0 72.384817 1 1 95.0 72.959465 1 1 96.0 73.530736 0 0 97.0 74.09865 1 1 98.0 74.663226 0 0 99.0 75.224485 0 0 100.0 75.782446 0 0 101.0 0 2 2 103.0 0 1 1 119.0 0 1 1 130.0 0 1 1 154.0 0 1 1 171.0 0 1 1 174.0 0 1 1 181.0 0 1 1 203.0 0 1 1 273.0 0 1 1 411.0 0 1 1