## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/PrC_14/PrC_14_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/PrC_14/PrC_14_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/PrC_14/PrC_14_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 60423 23033627 6359360 86025 44798 13867980 267136 0.602258 10292564 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.00315 4181367 0 4207554 2.0 1.110169 1949680 134162 1957538 3.0 1.121587 1109583 24681 1110327 4.0 1.122805 674052 9929 671427 5.0 1.122935 422511 4661 418110 6.0 1.122948 271110 2265 266440 7.0 1.12295 176853 1221 172861 8.0 1.12295 118127 672 114199 9.0 1.12295 79707 397 76483 10.0 1.12295 54191 234 51555 11.0 1.12295 37497 169 35473 12.0 1.12295 25833 95 24241 13.0 1.12295 18302 65 17061 14.0 1.12295 12819 49 11844 15.0 1.12295 9228 24 8431 16.0 1.12295 6595 19 5989 17.0 1.12295 4697 22 4265 18.0 1.12295 3577 17 3230 19.0 1.12295 2569 11 2291 20.0 1.12295 1887 11 1672 21.0 1.12295 1387 12 1192 22.0 1.12295 988 5 879 23.0 1.12295 762 4 666 24.0 1.12295 596 3 530 25.0 1.12295 427 1 346 26.0 1.12295 308 3 255 27.0 1.12295 245 1 202 28.0 1.12295 199 0 167 29.0 1.12295 110 2 88 30.0 1.12295 109 0 73 31.0 1.12295 81 0 61 32.0 1.12295 45 0 41 33.0 1.12295 45 0 42 34.0 1.12295 38 0 19 35.0 1.12295 30 0 20 36.0 1.12295 21 0 22 37.0 1.12295 15 0 9 38.0 1.12295 7 0 7 39.0 1.12295 10 0 4 40.0 1.12295 5 0 7 41.0 1.12295 3 1 1 42.0 1.12295 5 0 3 43.0 1.12295 1 0 1 44.0 1.12295 2 0 2 45.0 1.12295 2 0 1 46.0 1.12295 4 0 4 47.0 1.12295 2 0 4 48.0 1.12295 1 0 0 49.0 1.12295 2 0 1 50.0 1.12295 1 0 1 51.0 1.12295 0 0 1 52.0 1.12295 1 0 0 53.0 1.12295 3 0 2 54.0 1.12295 1 0 0 55.0 1.12295 0 0 0 56.0 1.12295 1 0 1 57.0 1.12295 1 0 0 58.0 1.12295 0 0 0 59.0 1.12295 0 0 0 60.0 1.12295 0 0 0 61.0 1.12295 0 0 0 62.0 1.12295 0 0 0 63.0 1.12295 0 0 0 64.0 1.12295 0 0 1 65.0 1.12295 0 0 0 66.0 1.12295 1 0 0 67.0 1.12295 0 0 0 68.0 1.12295 0 0 0 69.0 1.12295 0 0 0 70.0 1.12295 0 0 0 71.0 1.12295 0 0 0 72.0 1.12295 0 0 0 73.0 1.12295 0 0 0 74.0 1.12295 0 0 0 75.0 1.12295 0 0 0 76.0 1.12295 0 0 0 77.0 1.12295 0 0 0 78.0 1.12295 0 0 0 79.0 1.12295 0 0 0 80.0 1.12295 0 0 0 81.0 1.12295 0 0 0 82.0 1.12295 0 0 0 83.0 1.12295 0 0 0 84.0 1.12295 0 0 0 85.0 1.12295 0 0 0 86.0 1.12295 0 0 0 87.0 1.12295 0 0 0 88.0 1.12295 0 0 0 89.0 1.12295 0 0 0 90.0 1.12295 0 0 0 91.0 1.12295 0 0 0 92.0 1.12295 0 0 0 93.0 1.12295 0 0 0 94.0 1.12295 0 0 0 95.0 1.12295 0 0 0 96.0 1.12295 0 0 0 97.0 1.12295 0 0 0 98.0 1.12295 0 0 0 99.0 1.12295 0 0 0 100.0 1.12295 0 0 0 144.0 0 1 0 1 147.0 0 1 0 1 155.0 0 0 0 1 156.0 0 1 0 0