## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/BC_105/BC_105_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/BC_105/BC_105_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/BC_105/BC_105_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 17:00:15 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 110515 56564771 23743988 131073 71589 18813948 617991 0.332917 66123819 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.006992 25714184 0 25882148 2.0 1.435061 7847753 335557 7830605 3.0 1.617032 2647604 52030 2602502 4.0 1.694388 945278 21222 908205 5.0 1.727271 353941 9647 328673 6.0 1.74125 139002 4810 122642 7.0 1.747192 55916 2586 45909 8.0 1.749718 24171 1414 18110 9.0 1.750792 10636 896 6993 10.0 1.751249 5136 510 2840 11.0 1.751443 2747 339 1220 12.0 1.751525 1573 222 526 13.0 1.75156 858 141 206 14.0 1.751575 543 111 114 15.0 1.751581 397 71 56 16.0 1.751584 252 58 23 17.0 1.751585 185 42 19 18.0 1.751586 140 27 5 19.0 1.751586 105 31 7 20.0 1.751586 81 19 7 21.0 1.751586 48 13 2 22.0 1.751586 63 14 3 23.0 1.751586 40 6 0 24.0 1.751586 27 5 1 25.0 1.751586 23 5 0 26.0 1.751586 19 10 1 27.0 1.751586 13 5 0 28.0 1.751586 13 3 0 29.0 1.751586 12 6 1 30.0 1.751586 4 1 0 31.0 1.751586 7 2 1 32.0 1.751586 6 2 0 33.0 1.751586 9 2 2 34.0 1.751586 3 2 0 35.0 1.751586 6 1 0 36.0 1.751586 5 0 0 37.0 1.751586 5 1 0 38.0 1.751586 1 0 0 39.0 1.751586 4 1 0 40.0 1.751586 2 2 0 41.0 1.751586 2 0 0 42.0 1.751586 1 0 0 43.0 1.751586 1 0 0 44.0 1.751586 0 0 0 45.0 1.751586 0 0 0 46.0 1.751586 1 0 0 47.0 1.751586 1 0 0 48.0 1.751586 0 0 0 49.0 1.751586 1 0 0 50.0 1.751586 1 0 0 51.0 1.751586 0 0 0 52.0 1.751586 0 0 0 53.0 1.751586 0 0 1 54.0 1.751586 0 0 0 55.0 1.751586 1 0 0 56.0 1.751586 0 0 0 57.0 1.751586 0 0 0 58.0 1.751586 0 0 0 59.0 1.751586 0 0 0 60.0 1.751586 0 0 0 61.0 1.751586 0 0 0 62.0 1.751586 0 0 1 63.0 1.751586 0 0 0 64.0 1.751586 0 0 0 65.0 1.751586 0 0 0 66.0 1.751586 0 0 0 67.0 1.751586 0 0 0 68.0 1.751586 0 0 0 69.0 1.751586 0 0 0 70.0 1.751586 0 0 0 71.0 1.751586 0 0 0 72.0 1.751586 0 0 0 73.0 1.751586 0 0 0 74.0 1.751586 0 0 0 75.0 1.751586 0 0 0 76.0 1.751586 0 0 0 77.0 1.751586 1 0 0 78.0 1.751586 0 0 0 79.0 1.751586 0 0 0 80.0 1.751586 0 0 0 81.0 1.751586 0 0 0 82.0 1.751586 0 0 0 83.0 1.751586 0 0 0 84.0 1.751586 0 0 0 85.0 1.751586 0 0 0 86.0 1.751586 0 0 0 87.0 1.751586 0 0 0 88.0 1.751586 0 0 0 89.0 1.751586 0 0 0 90.0 1.751586 0 0 0 91.0 1.751586 0 0 0 92.0 1.751586 0 0 0 93.0 1.751586 0 0 0 94.0 1.751586 0 0 0 95.0 1.751586 0 0 0 96.0 1.751586 0 0 0 97.0 1.751586 0 0 0 98.0 1.751586 1 0 0 99.0 1.751586 0 0 0 100.0 1.751586 0 0 0