## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/BC_122/BC_122_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/BC_122/BC_122_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/BC_122/BC_122_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 17:00:16 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 253635 69579081 21865605 261799 170574 20283455 692843 0.29221 96856644 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.006877 35225588 0 35449100 2.0 1.497775 9864440 404570 9821817 3.0 1.73711 2897733 56338 2831346 4.0 1.853797 879743 21957 832688 5.0 1.910687 277631 9784 249642 6.0 1.938424 91857 4761 75735 7.0 1.951947 32821 2374 23691 8.0 1.95854 12919 1340 7567 9.0 1.961754 5586 811 2492 10.0 1.963321 2769 437 910 11.0 1.964085 1495 296 317 12.0 1.964458 901 196 143 13.0 1.964639 589 142 58 14.0 1.964728 408 107 32 15.0 1.964771 247 73 16 16.0 1.964792 225 51 14 17.0 1.964802 150 28 7 18.0 1.964807 114 16 6 19.0 1.96481 81 14 6 20.0 1.964811 69 14 7 21.0 1.964812 52 22 5 22.0 1.964812 41 10 5 23.0 1.964812 23 7 4 24.0 1.964812 38 7 2 25.0 1.964812 15 3 3 26.0 1.964812 18 1 1 27.0 1.964812 10 3 2 28.0 1.964812 8 0 1 29.0 1.964812 15 2 1 30.0 1.964812 6 2 1 31.0 1.964812 5 1 1 32.0 1.964812 7 1 1 33.0 1.964812 1 0 1 34.0 1.964812 2 0 1 35.0 1.964812 4 1 1 36.0 1.964812 2 0 0 37.0 1.964812 1 0 1 38.0 1.964812 2 1 0 39.0 1.964812 1 2 0 40.0 1.964812 2 0 0 41.0 1.964812 2 0 0 42.0 1.964812 1 0 0 43.0 1.964812 0 1 0 44.0 1.964812 1 0 1 45.0 1.964812 0 0 0 46.0 1.964812 1 0 0 47.0 1.964812 1 0 0 48.0 1.964812 0 0 0 49.0 1.964812 0 0 0 50.0 1.964812 0 0 0 51.0 1.964812 0 0 0 52.0 1.964812 0 0 0 53.0 1.964812 0 0 0 54.0 1.964812 0 0 0 55.0 1.964812 0 0 0 56.0 1.964812 0 0 0 57.0 1.964812 0 0 0 58.0 1.964812 1 0 0 59.0 1.964812 0 0 0 60.0 1.964812 0 0 0 61.0 1.964812 0 0 0 62.0 1.964812 0 0 0 63.0 1.964812 0 0 0 64.0 1.964812 0 0 0 65.0 1.964812 0 0 0 66.0 1.964812 0 0 0 67.0 1.964812 0 0 0 68.0 1.964812 0 0 0 69.0 1.964812 0 0 0 70.0 1.964812 0 0 0 71.0 1.964812 0 0 0 72.0 1.964812 0 0 0 73.0 1.964812 0 0 0 74.0 1.964812 0 0 0 75.0 1.964812 0 0 0 76.0 1.964812 0 0 0 77.0 1.964812 0 0 0 78.0 1.964812 0 0 0 79.0 1.964812 0 0 0 80.0 1.964812 0 0 0 81.0 1.964812 0 0 0 82.0 1.964812 0 0 0 83.0 1.964812 0 0 0 84.0 1.964812 0 0 0 85.0 1.964812 0 0 0 86.0 1.964812 0 0 0 87.0 1.964812 0 0 0 88.0 1.964812 0 0 0 89.0 1.964812 0 0 0 90.0 1.964812 0 0 0 91.0 1.964812 0 0 0 92.0 1.964812 0 0 0 93.0 1.964812 0 0 0 94.0 1.964812 0 0 0 95.0 1.964812 0 0 0 96.0 1.964812 0 0 0 97.0 1.964812 0 0 0 98.0 1.964812 0 0 0 99.0 1.964812 0 0 0 100.0 1.964812 0 0 0