## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/StS_1/StS_1_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/StS_1/StS_1_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/StS_1/StS_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 17:00:15 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 131576 66997384 17906139 149964 101470 36948146 708588 0.551702 35563758 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.00362 14376530 0 14466458 2.0 1.156172 6927527 387573 6950794 3.0 1.17936 3719300 58418 3715202 4.0 1.182884 2081697 23718 2066443 5.0 1.18342 1189843 11302 1171545 6.0 1.183502 694054 5473 676998 7.0 1.183514 411588 3101 397256 8.0 1.183516 247569 1700 236206 9.0 1.183516 150898 942 142028 10.0 1.183516 92568 594 86497 11.0 1.183516 57388 380 52481 12.0 1.183516 36237 253 32795 13.0 1.183516 22610 170 19973 14.0 1.183516 14502 136 12697 15.0 1.183516 9183 82 7839 16.0 1.183516 5988 84 5039 17.0 1.183516 3935 58 3260 18.0 1.183516 2614 42 2086 19.0 1.183516 1680 28 1283 20.0 1.183516 1107 19 824 21.0 1.183516 750 14 542 22.0 1.183516 464 9 303 23.0 1.183516 330 11 222 24.0 1.183516 238 12 155 25.0 1.183516 174 4 102 26.0 1.183516 125 3 57 27.0 1.183516 71 2 43 28.0 1.183516 73 3 28 29.0 1.183516 52 3 21 30.0 1.183516 19 1 9 31.0 1.183516 21 0 9 32.0 1.183516 17 1 6 33.0 1.183516 14 1 7 34.0 1.183516 14 2 4 35.0 1.183516 9 1 3 36.0 1.183516 9 1 3 37.0 1.183516 8 0 3 38.0 1.183516 4 0 1 39.0 1.183516 6 1 3 40.0 1.183516 2 0 1 41.0 1.183516 2 1 1 42.0 1.183516 1 0 0 43.0 1.183516 4 0 3 44.0 1.183516 3 0 2 45.0 1.183516 0 0 1 46.0 1.183516 4 0 1 47.0 1.183516 0 0 0 48.0 1.183516 0 0 0 49.0 1.183516 1 0 0 50.0 1.183516 0 0 0 51.0 1.183516 1 0 0 52.0 1.183516 0 0 0 53.0 1.183516 0 0 1 54.0 1.183516 1 0 0 55.0 1.183516 1 0 1 56.0 1.183516 0 0 0 57.0 1.183516 0 0 0 58.0 1.183516 1 0 1 59.0 1.183516 0 0 0 60.0 1.183516 0 0 0 61.0 1.183516 0 0 0 62.0 1.183516 0 0 0 63.0 1.183516 0 0 0 64.0 1.183516 0 0 0 65.0 1.183516 0 0 0 66.0 1.183516 0 0 0 67.0 1.183516 0 0 0 68.0 1.183516 0 0 0 69.0 1.183516 0 0 0 70.0 1.183516 0 0 0 71.0 1.183516 0 0 0 72.0 1.183516 0 0 0 73.0 1.183516 0 0 0 74.0 1.183516 0 0 0 75.0 1.183516 0 0 0 76.0 1.183516 0 0 0 77.0 1.183516 0 0 0 78.0 1.183516 0 0 0 79.0 1.183516 0 1 0 80.0 1.183516 0 0 0 81.0 1.183516 0 0 0 82.0 1.183516 0 0 0 83.0 1.183516 0 0 0 84.0 1.183516 0 0 0 85.0 1.183516 0 0 0 86.0 1.183516 0 0 0 87.0 1.183516 0 0 0 88.0 1.183516 0 0 0 89.0 1.183516 0 0 0 90.0 1.183516 0 0 0 91.0 1.183516 0 0 0 92.0 1.183516 0 0 0 93.0 1.183516 0 0 0 94.0 1.183516 0 0 0 95.0 1.183516 0 0 0 96.0 1.183516 0 0 0 97.0 1.183516 0 0 0 98.0 1.183516 0 0 0 99.0 1.183516 0 0 0 100.0 1.183516 0 0 0 123.0 0 0 0 1 201.0 0 1 0 0