## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/BC_123/BC_123_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/BC_123/BC_123_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/BC_123/BC_123_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 17:00:03 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 270697 43186417 12044671 277539 146001 8475940 427037 0.197336 98826763 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.007965 28029333 0 28213894 2.0 1.659087 5329754 260716 5256241 3.0 2.079697 1051183 33689 996992 4.0 2.351401 219777 12464 192563 5.0 2.526916 52537 5547 39001 6.0 2.640295 15241 2556 8562 7.0 2.713535 5591 1407 2068 8.0 2.760846 2700 739 657 9.0 2.791408 1447 456 235 10.0 2.81115 932 257 97 11.0 2.823904 581 181 47 12.0 2.832142 402 106 32 13.0 2.837463 268 71 19 14.0 2.840901 181 47 10 15.0 2.843122 133 40 4 16.0 2.844556 81 23 8 17.0 2.845483 79 16 5 18.0 2.846082 54 18 5 19.0 2.846468 34 5 2 20.0 2.846718 38 7 5 21.0 2.846879 20 7 5 22.0 2.846984 18 3 4 23.0 2.847051 19 10 6 24.0 2.847095 11 2 2 25.0 2.847123 10 2 0 26.0 2.847141 6 0 1 27.0 2.847152 8 2 3 28.0 2.84716 6 3 1 29.0 2.847165 8 0 2 30.0 2.847168 5 2 3 31.0 2.84717 5 1 1 32.0 2.847171 0 2 0 33.0 2.847172 3 1 1 34.0 2.847173 1 0 0 35.0 2.847173 1 0 0 36.0 2.847173 2 0 0 37.0 2.847174 3 0 0 38.0 2.847174 0 0 0 39.0 2.847174 0 0 0 40.0 2.847174 2 0 0 41.0 2.847174 0 0 0 42.0 2.847174 1 0 0 43.0 2.847174 0 0 0 44.0 2.847174 0 0 0 45.0 2.847174 0 0 0 46.0 2.847174 0 0 0 47.0 2.847174 0 1 0 48.0 2.847174 0 0 0 49.0 2.847174 0 0 0 50.0 2.847174 0 0 0 51.0 2.847174 0 0 0 52.0 2.847174 0 0 0 53.0 2.847174 0 0 0 54.0 2.847174 0 0 0 55.0 2.847174 0 0 0 56.0 2.847174 0 0 0 57.0 2.847174 0 0 0 58.0 2.847174 1 0 0 59.0 2.847174 0 0 0 60.0 2.847174 0 0 0 61.0 2.847174 0 0 0 62.0 2.847174 0 0 0 63.0 2.847174 0 0 0 64.0 2.847174 0 0 0 65.0 2.847174 0 0 0 66.0 2.847174 0 0 0 67.0 2.847174 0 0 1 68.0 2.847174 0 0 0 69.0 2.847174 0 0 0 70.0 2.847174 0 0 0 71.0 2.847174 0 0 0 72.0 2.847174 0 0 0 73.0 2.847174 0 0 0 74.0 2.847174 0 0 0 75.0 2.847174 0 0 0 76.0 2.847174 0 0 0 77.0 2.847174 0 0 0 78.0 2.847174 0 0 0 79.0 2.847174 0 0 0 80.0 2.847174 0 0 0 81.0 2.847174 0 0 0 82.0 2.847174 0 0 0 83.0 2.847174 0 0 0 84.0 2.847174 0 0 0 85.0 2.847174 0 0 0 86.0 2.847174 0 0 0 87.0 2.847174 0 0 0 88.0 2.847174 1 0 0 89.0 2.847174 0 0 0 90.0 2.847174 0 0 0 91.0 2.847174 0 0 0 92.0 2.847174 0 0 0 93.0 2.847174 0 0 0 94.0 2.847174 0 0 0 95.0 2.847174 0 0 0 96.0 2.847174 0 0 0 97.0 2.847174 0 0 0 98.0 2.847174 0 0 0 99.0 2.847174 0 0 0 100.0 2.847174 0 0 0