## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1250_15/G1250_15_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1250_15/G1250_15_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1250_15/G1250_15_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: Fri Aug 29 15:40:45 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 34212 57772087 39577346 61870 7705 7064279 0 0.122309 216554042 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 44564529 44564529 2.0 1.765842 5343293 5343293 3.0 2.352357 695372 695372 4.0 2.801534 90559 90559 5.0 3.145533 12086 12086 6.0 3.408982 1686 1686 7.0 3.610743 226 226 8.0 3.765259 41 41 9.0 3.883595 6 6 10.0 3.974221 4 4 11.0 4.043626 4 4 12.0 4.09678 1 1 13.0 4.137487 0 0 14.0 4.168662 1 1 15.0 4.192538 0 0 16.0 4.210823 0 0 17.0 4.224826 0 0 18.0 4.23555 0 0 19.0 4.243763 0 0 20.0 4.250053 0 0 21.0 4.25487 0 0 22.0 4.258559 0 0 23.0 4.261385 0 0 24.0 4.263548 0 0 25.0 4.265205 0 0 26.0 4.266475 0 0 27.0 4.267446 0 0 28.0 4.268191 0 0 29.0 4.268761 0 0 30.0 4.269197 0 0 31.0 4.269532 0 0 32.0 4.269788 0 0 33.0 4.269984 0 0 34.0 4.270134 0 0 35.0 4.270249 0 0 36.0 4.270337 0 0 37.0 4.270405 0 0 38.0 4.270456 0 0 39.0 4.270496 0 0 40.0 4.270526 0 0 41.0 4.270549 0 0 42.0 4.270567 0 0 43.0 4.270581 0 0 44.0 4.270591 0 0 45.0 4.270599 0 0 46.0 4.270605 0 0 47.0 4.27061 0 0 48.0 4.270613 0 0 49.0 4.270616 0 0 50.0 4.270618 0 0 51.0 4.27062 0 0 52.0 4.270621 0 0 53.0 4.270622 0 0 54.0 4.270623 0 0 55.0 4.270623 0 0 56.0 4.270624 0 0 57.0 4.270624 0 0 58.0 4.270624 0 0 59.0 4.270625 0 0 60.0 4.270625 0 0 61.0 4.270625 0 0 62.0 4.270625 0 0 63.0 4.270625 0 0 64.0 4.270625 0 0 65.0 4.270625 0 0 66.0 4.270625 0 0 67.0 4.270625 0 0 68.0 4.270625 0 0 69.0 4.270625 0 0 70.0 4.270625 0 0 71.0 4.270625 0 0 72.0 4.270625 0 0 73.0 4.270625 0 0 74.0 4.270625 0 0 75.0 4.270625 0 0 76.0 4.270625 0 0 77.0 4.270625 0 0 78.0 4.270625 0 0 79.0 4.270625 0 0 80.0 4.270625 0 0 81.0 4.270625 0 0 82.0 4.270625 0 0 83.0 4.270625 0 0 84.0 4.270625 0 0 85.0 4.270625 0 0 86.0 4.270625 0 0 87.0 4.270625 0 0 88.0 4.270625 0 0 89.0 4.270625 0 0 90.0 4.270625 0 0 91.0 4.270625 0 0 92.0 4.270625 0 0 93.0 4.270625 0 0 94.0 4.270625 0 0 95.0 4.270625 0 0 96.0 4.270625 0 0 97.0 4.270625 0 0 98.0 4.270625 0 0 99.0 4.270625 0 0 100.0 4.270625 0 0