## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/AS_2/AS_2_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/AS_2/AS_2_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/AS_2/AS_2_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 120976 60709125 23580025 134230 78599 20268020 638536 0.334169 70555714 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.006709 27378126 0 27557691 2.0 1.432521 8539460 365946 8520119 3.0 1.612629 2888727 53273 2839501 4.0 1.688811 1021944 20659 981003 5.0 1.721033 373692 9139 346328 6.0 1.734663 140899 4457 124197 7.0 1.740428 54973 2283 44966 8.0 1.742866 22622 1232 16751 9.0 1.743897 9731 798 6247 10.0 1.744334 4579 462 2399 11.0 1.744518 2387 286 940 12.0 1.744596 1302 206 415 13.0 1.744629 770 108 183 14.0 1.744643 518 95 104 15.0 1.744649 327 59 69 16.0 1.744652 253 44 38 17.0 1.744653 162 41 23 18.0 1.744653 148 28 24 19.0 1.744653 108 17 20 20.0 1.744653 64 14 12 21.0 1.744653 53 13 11 22.0 1.744653 45 11 11 23.0 1.744653 32 11 3 24.0 1.744653 32 2 6 25.0 1.744653 26 2 7 26.0 1.744653 19 6 4 27.0 1.744653 18 2 5 28.0 1.744653 10 4 2 29.0 1.744653 11 2 1 30.0 1.744653 9 2 3 31.0 1.744653 4 1 1 32.0 1.744653 12 0 4 33.0 1.744653 7 0 3 34.0 1.744653 6 1 1 35.0 1.744653 3 1 2 36.0 1.744653 4 0 1 37.0 1.744653 3 0 0 38.0 1.744653 3 1 2 39.0 1.744653 2 0 1 40.0 1.744653 1 1 1 41.0 1.744653 3 0 2 42.0 1.744653 1 0 0 43.0 1.744653 0 0 0 44.0 1.744653 0 1 1 45.0 1.744653 0 0 1 46.0 1.744653 0 0 0 47.0 1.744653 1 0 0 48.0 1.744653 1 0 0 49.0 1.744653 2 1 1 50.0 1.744653 2 0 0 51.0 1.744653 0 0 1 52.0 1.744653 0 0 0 53.0 1.744653 0 0 0 54.0 1.744653 1 0 0 55.0 1.744653 1 0 0 56.0 1.744653 0 0 0 57.0 1.744653 0 0 0 58.0 1.744653 1 0 0 59.0 1.744653 0 0 0 60.0 1.744653 0 0 0 61.0 1.744653 0 0 0 62.0 1.744653 0 0 0 63.0 1.744653 0 0 0 64.0 1.744653 0 0 0 65.0 1.744653 0 0 0 66.0 1.744653 0 0 0 67.0 1.744653 0 0 0 68.0 1.744653 0 0 0 69.0 1.744653 0 0 0 70.0 1.744653 0 0 0 71.0 1.744653 0 0 0 72.0 1.744653 0 0 0 73.0 1.744653 0 0 0 74.0 1.744653 0 0 0 75.0 1.744653 0 0 0 76.0 1.744653 0 0 0 77.0 1.744653 0 0 0 78.0 1.744653 0 0 0 79.0 1.744653 0 0 0 80.0 1.744653 0 0 0 81.0 1.744653 0 0 0 82.0 1.744653 0 0 0 83.0 1.744653 0 0 0 84.0 1.744653 0 0 0 85.0 1.744653 0 0 0 86.0 1.744653 0 0 0 87.0 1.744653 0 0 0 88.0 1.744653 0 0 0 89.0 1.744653 0 0 0 90.0 1.744653 0 0 0 91.0 1.744653 0 0 0 92.0 1.744653 0 0 0 93.0 1.744653 0 0 0 94.0 1.744653 0 0 0 95.0 1.744653 0 0 0 96.0 1.744653 0 0 0 97.0 1.744653 0 0 0 98.0 1.744653 0 0 0 99.0 1.744653 0 0 0 100.0 1.744653 0 0 0