## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_16/ALK_16_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_16/ALK_16_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_16/ALK_16_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 134603 61710343 24997740 154029 92733 25533710 648188 0.414067 52759800 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.005597 21864046 0 22004031 2.0 1.317812 8200159 365312 8205190 3.0 1.414747 3395033 53918 3364433 4.0 1.444843 1476184 21049 1443499 5.0 1.454187 660226 9645 634066 6.0 1.457088 302592 4744 283795 7.0 1.457989 141877 2472 129297 8.0 1.458269 68078 1435 59427 9.0 1.458355 32821 852 27701 10.0 1.458382 16268 484 12869 11.0 1.458391 8594 318 6367 12.0 1.458393 4453 223 2928 13.0 1.458394 2420 134 1442 14.0 1.458394 1373 81 747 15.0 1.458394 822 72 345 16.0 1.458394 493 55 190 17.0 1.458394 294 40 91 18.0 1.458394 227 32 45 19.0 1.458394 142 25 43 20.0 1.458394 102 15 30 21.0 1.458394 82 13 24 22.0 1.458394 69 15 15 23.0 1.458394 49 4 10 24.0 1.458394 42 4 6 25.0 1.458394 36 6 5 26.0 1.458394 35 1 9 27.0 1.458394 24 4 5 28.0 1.458394 17 2 5 29.0 1.458394 9 3 2 30.0 1.458394 13 4 3 31.0 1.458394 12 0 2 32.0 1.458394 4 1 1 33.0 1.458394 6 0 1 34.0 1.458394 2 0 0 35.0 1.458394 2 1 2 36.0 1.458394 4 1 0 37.0 1.458394 4 1 1 38.0 1.458394 2 0 1 39.0 1.458394 3 0 1 40.0 1.458394 2 0 0 41.0 1.458394 1 2 1 42.0 1.458394 1 0 1 43.0 1.458394 0 0 0 44.0 1.458394 1 0 0 45.0 1.458394 1 0 0 46.0 1.458394 1 0 0 47.0 1.458394 0 0 0 48.0 1.458394 1 0 0 49.0 1.458394 1 0 0 50.0 1.458394 0 0 1 51.0 1.458394 2 0 0 52.0 1.458394 1 0 0 53.0 1.458394 1 0 0 54.0 1.458394 0 0 0 55.0 1.458394 1 0 1 56.0 1.458394 0 0 0 57.0 1.458394 0 0 0 58.0 1.458394 0 0 0 59.0 1.458394 0 0 0 60.0 1.458394 0 0 0 61.0 1.458394 0 0 0 62.0 1.458394 0 0 0 63.0 1.458394 0 0 0 64.0 1.458394 0 0 0 65.0 1.458394 0 0 0 66.0 1.458394 0 0 0 67.0 1.458394 0 0 0 68.0 1.458394 0 0 0 69.0 1.458394 0 0 0 70.0 1.458394 0 0 0 71.0 1.458394 0 0 0 72.0 1.458394 0 0 0 73.0 1.458394 0 0 0 74.0 1.458394 0 0 0 75.0 1.458394 0 0 0 76.0 1.458394 0 0 0 77.0 1.458394 0 0 0 78.0 1.458394 0 0 0 79.0 1.458394 0 0 0 80.0 1.458394 0 0 0 81.0 1.458394 0 0 0 82.0 1.458394 0 0 0 83.0 1.458394 0 0 0 84.0 1.458394 0 0 0 85.0 1.458394 0 0 0 86.0 1.458394 0 0 0 87.0 1.458394 0 0 0 88.0 1.458394 0 0 0 89.0 1.458394 0 0 0 90.0 1.458394 0 0 0 91.0 1.458394 0 0 0 92.0 1.458394 0 0 0 93.0 1.458394 0 0 0 94.0 1.458394 0 0 0 95.0 1.458394 0 0 0 96.0 1.458394 0 0 0 97.0 1.458394 0 0 0 98.0 1.458394 0 0 0 99.0 1.458394 0 0 0 100.0 1.458394 0 0 0