## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/NC_3/NC_3_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/NC_3/NC_3_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/NC_3/NC_3_dedup_metrics.txt CREATE_INDEX=true 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 FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false 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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Thu Aug 28 17:00:17 NOVT 2025 ## 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 Unknown Library 152563 67647529 22002536 163541 105815 29348812 662767 0.434142 53768491 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.004948 22445963 0 22586739 2.0 1.290541 8774404 398748 8780936 3.0 1.371702 3791946 54005 3762873 4.0 1.394767 1714969 20531 1681833 5.0 1.401322 804225 8952 777398 6.0 1.403185 385755 4040 365891 7.0 1.403714 187665 2141 174696 8.0 1.403864 93637 1125 84733 9.0 1.403907 47927 629 42048 10.0 1.403919 24438 384 20606 11.0 1.403923 12596 209 10353 12.0 1.403924 6673 154 5179 13.0 1.403924 3621 102 2610 14.0 1.403924 2006 72 1351 15.0 1.403924 1111 53 688 16.0 1.403924 644 43 374 17.0 1.403924 371 24 185 18.0 1.403924 256 15 102 19.0 1.403924 140 13 54 20.0 1.403924 97 10 27 21.0 1.403924 82 7 18 22.0 1.403924 44 4 14 23.0 1.403924 38 5 5 24.0 1.403924 23 3 1 25.0 1.403924 24 3 2 26.0 1.403924 13 2 0 27.0 1.403924 6 2 0 28.0 1.403924 6 1 0 29.0 1.403924 4 2 0 30.0 1.403924 9 0 0 31.0 1.403924 3 0 0 32.0 1.403924 3 0 0 33.0 1.403924 5 0 0 34.0 1.403924 1 2 0 35.0 1.403924 0 1 1 36.0 1.403924 5 0 0 37.0 1.403924 1 0 0 38.0 1.403924 2 0 0 39.0 1.403924 0 0 0 40.0 1.403924 0 0 0 41.0 1.403924 0 0 0 42.0 1.403924 0 0 0 43.0 1.403924 0 0 0 44.0 1.403924 1 0 0 45.0 1.403924 0 0 0 46.0 1.403924 1 1 0 47.0 1.403924 1 0 0 48.0 1.403924 0 0 0 49.0 1.403924 0 0 0 50.0 1.403924 0 0 0 51.0 1.403924 0 0 0 52.0 1.403924 0 0 0 53.0 1.403924 0 0 0 54.0 1.403924 1 0 0 55.0 1.403924 0 0 0 56.0 1.403924 0 0 0 57.0 1.403924 0 0 0 58.0 1.403924 0 0 0 59.0 1.403924 0 0 0 60.0 1.403924 0 0 0 61.0 1.403924 0 0 0 62.0 1.403924 0 0 0 63.0 1.403924 0 0 0 64.0 1.403924 0 0 0 65.0 1.403924 0 0 0 66.0 1.403924 0 0 0 67.0 1.403924 0 0 0 68.0 1.403924 0 0 0 69.0 1.403924 0 0 0 70.0 1.403924 0 0 0 71.0 1.403924 0 0 0 72.0 1.403924 0 0 0 73.0 1.403924 0 0 0 74.0 1.403924 0 0 0 75.0 1.403924 0 0 0 76.0 1.403924 0 0 0 77.0 1.403924 0 0 0 78.0 1.403924 0 0 0 79.0 1.403924 0 0 0 80.0 1.403924 0 0 0 81.0 1.403924 0 0 0 82.0 1.403924 0 0 0 83.0 1.403924 0 0 0 84.0 1.403924 0 0 0 85.0 1.403924 0 0 0 86.0 1.403924 0 0 0 87.0 1.403924 0 0 0 88.0 1.403924 0 0 0 89.0 1.403924 0 0 0 90.0 1.403924 0 0 0 91.0 1.403924 0 0 0 92.0 1.403924 0 0 0 93.0 1.403924 0 0 0 94.0 1.403924 0 0 0 95.0 1.403924 0 0 0 96.0 1.403924 0 0 0 97.0 1.403924 0 0 0 98.0 1.403924 0 0 0 99.0 1.403924 0 0 0 100.0 1.403924 0 0 0