## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/NS_29/NS_29_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/NS_29/NS_29_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/NS_29/NS_29_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 17:00:16 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 27180 11466301 2512598 35608 20029 7226558 137497 0.630369 4645058 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.002788 1794299 0 1805910 2.0 1.087737 893291 68989 897396 3.0 1.094933 533711 12142 534788 4.0 1.095543 338672 4955 337716 5.0 1.095594 219304 2305 217625 6.0 1.095599 144374 1210 142382 7.0 1.095599 97144 642 95119 8.0 1.095599 66133 391 64241 9.0 1.095599 45193 235 43566 10.0 1.095599 31295 137 30069 11.0 1.095599 21894 91 20717 12.0 1.095599 15246 62 14428 13.0 1.095599 10879 39 10123 14.0 1.095599 7863 28 7313 15.0 1.095599 5521 23 5155 16.0 1.095599 4057 19 3714 17.0 1.095599 3000 11 2676 18.0 1.095599 2141 7 1932 19.0 1.095599 1496 9 1299 20.0 1.095599 1152 8 1004 21.0 1.095599 786 7 715 22.0 1.095599 601 1 509 23.0 1.095599 425 3 350 24.0 1.095599 315 4 257 25.0 1.095599 238 2 200 26.0 1.095599 163 3 136 27.0 1.095599 125 1 91 28.0 1.095599 105 3 89 29.0 1.095599 65 1 48 30.0 1.095599 59 0 40 31.0 1.095599 46 0 30 32.0 1.095599 39 2 34 33.0 1.095599 34 0 19 34.0 1.095599 14 1 15 35.0 1.095599 12 1 7 36.0 1.095599 8 0 6 37.0 1.095599 9 0 10 38.0 1.095599 9 0 2 39.0 1.095599 4 0 1 40.0 1.095599 4 0 3 41.0 1.095599 0 0 1 42.0 1.095599 5 1 2 43.0 1.095599 1 0 0 44.0 1.095599 0 0 0 45.0 1.095599 2 0 0 46.0 1.095599 2 0 0 47.0 1.095599 1 0 1 48.0 1.095599 0 0 0 49.0 1.095599 1 0 1 50.0 1.095599 0 0 1 51.0 1.095599 1 0 0 52.0 1.095599 0 0 0 53.0 1.095599 0 0 0 54.0 1.095599 0 0 0 55.0 1.095599 0 0 0 56.0 1.095599 1 0 1 57.0 1.095599 2 0 0 58.0 1.095599 0 0 0 59.0 1.095599 0 0 0 60.0 1.095599 0 0 0 61.0 1.095599 0 0 0 62.0 1.095599 0 0 0 63.0 1.095599 0 0 0 64.0 1.095599 0 0 0 65.0 1.095599 0 0 0 66.0 1.095599 0 0 0 67.0 1.095599 0 0 0 68.0 1.095599 0 0 0 69.0 1.095599 0 0 0 70.0 1.095599 0 0 0 71.0 1.095599 0 0 0 72.0 1.095599 0 0 0 73.0 1.095599 0 0 0 74.0 1.095599 0 0 1 75.0 1.095599 0 0 0 76.0 1.095599 0 0 0 77.0 1.095599 0 0 0 78.0 1.095599 0 0 0 79.0 1.095599 0 0 0 80.0 1.095599 0 0 0 81.0 1.095599 0 0 0 82.0 1.095599 0 0 0 83.0 1.095599 0 0 0 84.0 1.095599 0 0 0 85.0 1.095599 0 0 0 86.0 1.095599 0 0 0 87.0 1.095599 0 0 0 88.0 1.095599 0 0 0 89.0 1.095599 0 0 0 90.0 1.095599 0 0 0 91.0 1.095599 0 0 0 92.0 1.095599 0 0 0 93.0 1.095599 0 0 0 94.0 1.095599 0 0 0 95.0 1.095599 0 0 0 96.0 1.095599 0 0 0 97.0 1.095599 0 0 0 98.0 1.095599 0 0 0 99.0 1.095599 0 0 0 100.0 1.095599 0 0 0 108.0 0 1 0 0