## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/StS_5/StS_5_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/StS_5/StS_5_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/StS_5/StS_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 17:00:16 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 104372 53709643 22877939 122590 70320 22003420 561609 0.40993 46606666 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.005629 19433058 0 19553673 2.0 1.323284 7051316 305928 7055033 3.0 1.423624 2880238 47320 2853955 4.0 1.455319 1249791 19321 1221903 5.0 1.465331 566939 9002 544869 6.0 1.468493 265032 4493 249581 7.0 1.469492 127932 2267 117036 8.0 1.469808 63423 1313 56049 9.0 1.469907 31774 761 26896 10.0 1.469939 16458 434 13294 11.0 1.469949 8662 277 6648 12.0 1.469952 4707 172 3437 13.0 1.469953 2702 149 1783 14.0 1.469953 1552 71 935 15.0 1.469953 857 55 448 16.0 1.469953 507 51 218 17.0 1.469953 341 34 143 18.0 1.469953 241 24 98 19.0 1.469953 167 19 58 20.0 1.469953 117 21 32 21.0 1.469953 94 6 27 22.0 1.469953 53 11 16 23.0 1.469953 55 6 11 24.0 1.469953 36 6 15 25.0 1.469953 26 3 11 26.0 1.469953 19 5 7 27.0 1.469953 21 3 9 28.0 1.469953 20 1 5 29.0 1.469953 19 2 8 30.0 1.469953 10 2 3 31.0 1.469953 8 1 4 32.0 1.469953 11 0 2 33.0 1.469953 6 1 3 34.0 1.469953 5 1 1 35.0 1.469953 1 0 1 36.0 1.469953 4 1 0 37.0 1.469953 3 0 1 38.0 1.469953 1 0 0 39.0 1.469953 5 0 2 40.0 1.469953 0 0 0 41.0 1.469953 2 0 1 42.0 1.469953 1 0 2 43.0 1.469953 2 0 1 44.0 1.469953 0 0 0 45.0 1.469953 3 0 0 46.0 1.469953 0 0 0 47.0 1.469953 0 0 0 48.0 1.469953 0 0 0 49.0 1.469953 0 0 0 50.0 1.469953 0 0 1 51.0 1.469953 2 1 1 52.0 1.469953 0 0 0 53.0 1.469953 0 0 0 54.0 1.469953 0 0 0 55.0 1.469953 0 0 0 56.0 1.469953 0 0 1 57.0 1.469953 0 0 0 58.0 1.469953 0 0 0 59.0 1.469953 0 0 0 60.0 1.469953 0 0 0 61.0 1.469953 0 0 0 62.0 1.469953 0 0 0 63.0 1.469953 0 0 1 64.0 1.469953 1 0 0 65.0 1.469953 0 0 0 66.0 1.469953 0 0 0 67.0 1.469953 0 0 0 68.0 1.469953 0 0 0 69.0 1.469953 0 0 0 70.0 1.469953 0 0 0 71.0 1.469953 0 0 0 72.0 1.469953 0 0 0 73.0 1.469953 0 0 0 74.0 1.469953 0 0 0 75.0 1.469953 0 0 0 76.0 1.469953 0 0 0 77.0 1.469953 0 0 0 78.0 1.469953 0 0 0 79.0 1.469953 0 0 0 80.0 1.469953 0 0 0 81.0 1.469953 0 0 0 82.0 1.469953 0 0 0 83.0 1.469953 0 0 0 84.0 1.469953 0 0 0 85.0 1.469953 0 0 0 86.0 1.469953 0 0 0 87.0 1.469953 0 0 0 88.0 1.469953 0 0 0 89.0 1.469953 0 0 0 90.0 1.469953 0 0 0 91.0 1.469953 0 0 0 92.0 1.469953 0 0 0 93.0 1.469953 0 0 0 94.0 1.469953 0 0 0 95.0 1.469953 0 0 0 96.0 1.469953 0 0 0 97.0 1.469953 0 0 0 98.0 1.469953 0 0 0 99.0 1.469953 0 0 0 100.0 1.469953 0 0 0 106.0 0 1 0 0