## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_5/ALK_5_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_5/ALK_5_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_5/ALK_5_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 17:00:15 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 77969 27087116 8928272 99559 56993 15433312 318717 0.569997 13521131 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.003733 5684234 0 5720975 2.0 1.139123 2545966 161218 2554738 3.0 1.157386 1349164 28236 1348515 4.0 1.159849 770218 11636 764512 5.0 1.160181 460426 5557 453863 6.0 1.160226 285170 2809 278887 7.0 1.160232 182651 1503 176874 8.0 1.160233 118663 853 114214 9.0 1.160233 78668 455 75271 10.0 1.160233 53667 301 50737 11.0 1.160233 36486 205 34242 12.0 1.160233 25147 140 23544 13.0 1.160233 17879 79 16497 14.0 1.160233 12706 62 11709 15.0 1.160233 9075 38 8310 16.0 1.160233 6279 34 5664 17.0 1.160233 4557 19 4073 18.0 1.160233 3338 24 2984 19.0 1.160233 2450 10 2189 20.0 1.160233 1841 11 1603 21.0 1.160233 1344 12 1192 22.0 1.160233 962 3 811 23.0 1.160233 749 7 647 24.0 1.160233 556 6 470 25.0 1.160233 402 2 345 26.0 1.160233 315 5 246 27.0 1.160233 211 1 180 28.0 1.160233 170 3 131 29.0 1.160233 114 0 92 30.0 1.160233 99 1 68 31.0 1.160233 65 0 58 32.0 1.160233 71 0 44 33.0 1.160233 34 1 33 34.0 1.160233 31 1 20 35.0 1.160233 15 0 14 36.0 1.160233 12 0 8 37.0 1.160233 12 0 6 38.0 1.160233 13 0 10 39.0 1.160233 10 0 5 40.0 1.160233 6 0 2 41.0 1.160233 5 0 3 42.0 1.160233 2 0 1 43.0 1.160233 2 0 1 44.0 1.160233 1 0 1 45.0 1.160233 1 0 0 46.0 1.160233 1 0 1 47.0 1.160233 0 0 0 48.0 1.160233 2 0 2 49.0 1.160233 0 0 0 50.0 1.160233 2 0 2 51.0 1.160233 0 0 0 52.0 1.160233 0 0 0 53.0 1.160233 0 1 0 54.0 1.160233 0 0 0 55.0 1.160233 2 0 2 56.0 1.160233 0 0 0 57.0 1.160233 0 0 0 58.0 1.160233 0 0 0 59.0 1.160233 1 0 0 60.0 1.160233 0 0 0 61.0 1.160233 0 0 0 62.0 1.160233 0 0 0 63.0 1.160233 0 0 0 64.0 1.160233 0 0 0 65.0 1.160233 0 0 0 66.0 1.160233 0 0 0 67.0 1.160233 1 0 0 68.0 1.160233 0 0 0 69.0 1.160233 0 0 0 70.0 1.160233 0 0 0 71.0 1.160233 0 0 0 72.0 1.160233 0 0 0 73.0 1.160233 0 0 0 74.0 1.160233 0 0 0 75.0 1.160233 0 0 0 76.0 1.160233 2 0 2 77.0 1.160233 0 0 0 78.0 1.160233 0 0 0 79.0 1.160233 0 0 0 80.0 1.160233 0 0 0 81.0 1.160233 0 0 0 82.0 1.160233 0 0 0 83.0 1.160233 0 0 0 84.0 1.160233 0 0 0 85.0 1.160233 0 0 0 86.0 1.160233 1 0 1 87.0 1.160233 0 0 0 88.0 1.160233 0 0 0 89.0 1.160233 0 0 0 90.0 1.160233 0 0 0 91.0 1.160233 1 0 1 92.0 1.160233 0 0 0 93.0 1.160233 0 0 0 94.0 1.160233 0 0 0 95.0 1.160233 0 0 0 96.0 1.160233 0 0 0 97.0 1.160233 0 0 0 98.0 1.160233 0 0 0 99.0 1.160233 0 0 0 100.0 1.160233 0 0 0 174.0 0 1 0 1 189.0 0 1 0 1 191.0 0 1 0 1 215.0 0 1 0 1