## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_8/ALK_8_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_8/ALK_8_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_8/ALK_8_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 17:00:05 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 275899 45849496 13444076 281305 172448 12826278 461574 0.280783 67365390 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.007101 23970930 0 24129657 2.0 1.517005 6458224 281595 6421615 3.0 1.775174 1817402 35435 1768539 4.0 1.905887 530612 13410 499340 5.0 1.972068 161287 6138 143237 6.0 2.005576 51979 2921 42070 7.0 2.022541 17939 1493 12503 8.0 2.031131 7103 824 3963 9.0 2.03548 3172 462 1337 10.0 2.037682 1590 318 474 11.0 2.038797 948 181 183 12.0 2.039361 563 130 79 13.0 2.039647 366 99 50 14.0 2.039792 257 55 31 15.0 2.039865 203 43 22 16.0 2.039902 120 37 17 17.0 2.039921 96 24 10 18.0 2.03993 73 19 7 19.0 2.039935 72 10 7 20.0 2.039938 54 8 14 21.0 2.039939 34 10 5 22.0 2.03994 25 8 4 23.0 2.03994 29 7 9 24.0 2.03994 23 4 2 25.0 2.03994 16 4 4 26.0 2.03994 13 3 5 27.0 2.03994 6 3 3 28.0 2.03994 7 3 1 29.0 2.03994 8 2 0 30.0 2.03994 10 1 1 31.0 2.03994 9 0 1 32.0 2.03994 5 0 1 33.0 2.03994 4 0 3 34.0 2.03994 8 1 3 35.0 2.03994 7 0 3 36.0 2.03994 3 0 3 37.0 2.03994 0 0 0 38.0 2.03994 4 1 1 39.0 2.03994 1 0 1 40.0 2.03994 0 0 0 41.0 2.03994 1 0 1 42.0 2.03994 1 0 0 43.0 2.03994 1 0 1 44.0 2.03994 0 0 0 45.0 2.03994 2 0 1 46.0 2.03994 1 0 1 47.0 2.03994 0 0 0 48.0 2.03994 1 0 1 49.0 2.03994 1 0 1 50.0 2.03994 0 0 0 51.0 2.03994 0 0 0 52.0 2.03994 0 0 0 53.0 2.03994 0 0 0 54.0 2.03994 0 0 0 55.0 2.03994 0 0 1 56.0 2.03994 1 0 1 57.0 2.03994 0 0 0 58.0 2.03994 1 0 1 59.0 2.03994 0 0 0 60.0 2.03994 1 0 1 61.0 2.03994 0 0 0 62.0 2.03994 0 0 0 63.0 2.03994 0 0 0 64.0 2.03994 0 0 0 65.0 2.03994 0 0 0 66.0 2.03994 0 0 1 67.0 2.03994 0 0 0 68.0 2.03994 0 0 0 69.0 2.03994 1 0 0 70.0 2.03994 0 0 0 71.0 2.03994 1 0 0 72.0 2.03994 0 0 0 73.0 2.03994 0 0 0 74.0 2.03994 0 0 0 75.0 2.03994 0 0 0 76.0 2.03994 0 0 0 77.0 2.03994 0 0 0 78.0 2.03994 1 0 0 79.0 2.03994 1 0 1 80.0 2.03994 0 0 0 81.0 2.03994 0 0 0 82.0 2.03994 0 0 1 83.0 2.03994 1 0 0 84.0 2.03994 0 0 0 85.0 2.03994 0 0 0 86.0 2.03994 0 0 0 87.0 2.03994 0 0 0 88.0 2.03994 0 0 0 89.0 2.03994 0 0 0 90.0 2.03994 0 0 0 91.0 2.03994 0 0 0 92.0 2.03994 0 0 0 93.0 2.03994 0 0 0 94.0 2.03994 0 0 0 95.0 2.03994 0 0 0 96.0 2.03994 0 0 0 97.0 2.03994 0 0 0 98.0 2.03994 0 0 0 99.0 2.03994 0 0 0 100.0 2.03994 0 0 0