## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/HE_1/HE_1_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/HE_1/HE_1_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/HE_1/HE_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 17:00:04 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 129247 64546910 23240281 145481 90560 28488199 667603 0.441616 49984050 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.005124 20998093 0 21130071 2.0 1.281432 8196853 378913 8205790 3.0 1.357388 3594592 53804 3569562 4.0 1.378269 1664047 21415 1634292 5.0 1.384009 799588 10106 774521 6.0 1.385587 394277 4919 374832 7.0 1.386021 197155 2589 183703 8.0 1.38614 100387 1481 91322 9.0 1.386173 52459 845 46136 10.0 1.386182 27588 528 23557 11.0 1.386184 14748 337 11973 12.0 1.386185 7959 218 6138 13.0 1.386185 4499 143 3172 14.0 1.386185 2514 91 1674 15.0 1.386185 1346 79 845 16.0 1.386185 865 72 466 17.0 1.386185 533 40 270 18.0 1.386185 352 38 140 19.0 1.386185 223 27 80 20.0 1.386185 145 16 38 21.0 1.386185 112 14 34 22.0 1.386185 76 11 19 23.0 1.386185 52 6 14 24.0 1.386185 54 9 7 25.0 1.386185 37 2 6 26.0 1.386185 19 3 6 27.0 1.386185 20 0 6 28.0 1.386185 26 4 5 29.0 1.386185 13 5 4 30.0 1.386185 11 4 7 31.0 1.386185 15 1 3 32.0 1.386185 10 0 2 33.0 1.386185 9 1 3 34.0 1.386185 4 0 2 35.0 1.386185 5 0 0 36.0 1.386185 3 0 1 37.0 1.386185 2 0 1 38.0 1.386185 3 0 0 39.0 1.386185 1 1 0 40.0 1.386185 2 1 2 41.0 1.386185 2 0 0 42.0 1.386185 2 0 2 43.0 1.386185 0 0 0 44.0 1.386185 2 0 1 45.0 1.386185 1 0 0 46.0 1.386185 1 0 1 47.0 1.386185 1 0 0 48.0 1.386185 0 0 0 49.0 1.386185 0 0 0 50.0 1.386185 2 0 2 51.0 1.386185 1 0 0 52.0 1.386185 0 0 0 53.0 1.386185 0 0 0 54.0 1.386185 1 0 0 55.0 1.386185 1 0 1 56.0 1.386185 0 0 0 57.0 1.386185 0 0 0 58.0 1.386185 0 0 0 59.0 1.386185 0 0 0 60.0 1.386185 0 0 0 61.0 1.386185 0 0 0 62.0 1.386185 0 0 0 63.0 1.386185 0 0 0 64.0 1.386185 0 0 0 65.0 1.386185 0 0 0 66.0 1.386185 0 0 0 67.0 1.386185 0 0 0 68.0 1.386185 0 0 0 69.0 1.386185 0 0 0 70.0 1.386185 0 0 0 71.0 1.386185 0 0 0 72.0 1.386185 0 0 0 73.0 1.386185 0 0 0 74.0 1.386185 0 0 0 75.0 1.386185 0 0 0 76.0 1.386185 0 0 0 77.0 1.386185 0 0 0 78.0 1.386185 0 0 0 79.0 1.386185 0 0 0 80.0 1.386185 0 0 0 81.0 1.386185 0 0 0 82.0 1.386185 0 0 0 83.0 1.386185 0 0 0 84.0 1.386185 0 0 0 85.0 1.386185 0 0 0 86.0 1.386185 0 0 0 87.0 1.386185 0 0 0 88.0 1.386185 0 0 0 89.0 1.386185 0 0 0 90.0 1.386185 0 0 0 91.0 1.386185 0 0 0 92.0 1.386185 0 0 0 93.0 1.386185 0 0 0 94.0 1.386185 0 0 0 95.0 1.386185 0 0 0 96.0 1.386185 0 0 0 97.0 1.386185 0 0 0 98.0 1.386185 0 0 0 99.0 1.386185 0 0 0 100.0 1.386185 0 0 0