## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ES_1/ES_1_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ES_1/ES_1_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ES_1/ES_1_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 141927 55720977 21209405 152839 85182 14206968 555509 0.255405 92194412 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.007334 31198560 0 31398722 2.0 1.557751 7581107 329041 7528035 3.0 1.858504 1963255 45452 1902166 4.0 2.022839 535545 17121 497882 5.0 2.112633 155160 7571 134162 6.0 2.161698 48760 3622 37474 7.0 2.188507 16978 1862 10569 8.0 2.203156 6843 1006 3314 9.0 2.21116 3186 559 1079 10.0 2.215534 1637 355 340 11.0 2.217924 897 222 146 12.0 2.219229 625 167 53 13.0 2.219943 395 100 39 14.0 2.220333 274 76 10 15.0 2.220546 197 54 6 16.0 2.220662 119 37 3 17.0 2.220726 107 23 3 18.0 2.220761 87 18 1 19.0 2.22078 54 19 3 20.0 2.22079 50 17 1 21.0 2.220796 40 10 0 22.0 2.220799 25 8 0 23.0 2.2208 19 5 0 24.0 2.220801 16 5 0 25.0 2.220802 18 1 0 26.0 2.220802 10 1 0 27.0 2.220802 11 2 0 28.0 2.220802 6 0 0 29.0 2.220802 5 3 0 30.0 2.220802 2 1 0 31.0 2.220802 1 0 0 32.0 2.220802 5 0 0 33.0 2.220802 2 0 0 34.0 2.220802 5 1 0 35.0 2.220802 3 0 0 36.0 2.220802 0 0 0 37.0 2.220802 0 0 0 38.0 2.220802 1 0 0 39.0 2.220802 0 0 0 40.0 2.220802 1 0 0 41.0 2.220802 0 0 0 42.0 2.220802 1 1 0 43.0 2.220802 0 0 0 44.0 2.220802 0 0 0 45.0 2.220802 0 0 0 46.0 2.220802 1 0 0 47.0 2.220802 0 0 0 48.0 2.220802 0 0 0 49.0 2.220802 0 0 0 50.0 2.220802 0 0 0 51.0 2.220802 0 0 0 52.0 2.220802 0 0 0 53.0 2.220802 0 0 0 54.0 2.220802 0 0 0 55.0 2.220802 0 0 0 56.0 2.220802 0 0 0 57.0 2.220802 0 0 0 58.0 2.220802 0 0 0 59.0 2.220802 0 0 0 60.0 2.220802 0 0 0 61.0 2.220802 0 0 0 62.0 2.220802 0 0 0 63.0 2.220802 0 0 0 64.0 2.220802 0 0 0 65.0 2.220802 0 0 0 66.0 2.220802 0 0 0 67.0 2.220802 0 0 0 68.0 2.220802 0 0 0 69.0 2.220802 0 0 0 70.0 2.220802 0 0 0 71.0 2.220802 0 0 0 72.0 2.220802 0 0 0 73.0 2.220802 0 0 0 74.0 2.220802 0 0 0 75.0 2.220802 0 0 0 76.0 2.220802 0 0 0 77.0 2.220802 0 0 0 78.0 2.220802 0 0 0 79.0 2.220802 0 0 0 80.0 2.220802 0 0 0 81.0 2.220802 0 0 0 82.0 2.220802 0 0 0 83.0 2.220802 0 0 0 84.0 2.220802 0 0 0 85.0 2.220802 0 0 0 86.0 2.220802 0 0 0 87.0 2.220802 0 0 0 88.0 2.220802 0 0 0 89.0 2.220802 0 0 0 90.0 2.220802 0 0 0 91.0 2.220802 0 0 0 92.0 2.220802 0 0 0 93.0 2.220802 0 0 0 94.0 2.220802 0 0 0 95.0 2.220802 0 0 0 96.0 2.220802 0 0 0 97.0 2.220802 0 0 0 98.0 2.220802 0 0 0 99.0 2.220802 0 0 0 100.0 2.220802 0 0 0 151.0 0 0 1 0 217.0 0 0 0 1 367.0 0 1 0 0