## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ChC_13/ChC_13_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ChC_13/ChC_13_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ChC_13/ChC_13_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 114948 56412285 20003637 129366 77813 23993817 589376 0.425586 46255239 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.005404 19272945 0 19396145 2.0 1.302352 7373582 337050 7378520 3.0 1.390056 3135384 46900 3110411 4.0 1.41596 1397606 18653 1369343 5.0 1.423611 644261 8785 621392 6.0 1.42587 302788 4293 285710 7.0 1.426538 145383 2238 133494 8.0 1.426735 71718 1322 63892 9.0 1.426793 35404 766 30349 10.0 1.42681 18046 449 14835 11.0 1.426815 9457 306 7220 12.0 1.426817 4922 219 3516 13.0 1.426817 2771 135 1797 14.0 1.426817 1599 93 924 15.0 1.426818 891 68 439 16.0 1.426818 529 47 222 17.0 1.426818 363 39 119 18.0 1.426818 246 26 66 19.0 1.426818 156 22 37 20.0 1.426818 99 14 17 21.0 1.426818 66 9 7 22.0 1.426818 40 13 4 23.0 1.426818 38 4 2 24.0 1.426818 31 5 2 25.0 1.426818 36 6 0 26.0 1.426818 19 5 2 27.0 1.426818 9 4 0 28.0 1.426818 19 3 0 29.0 1.426818 8 1 0 30.0 1.426818 5 2 0 31.0 1.426818 7 3 0 32.0 1.426818 5 0 0 33.0 1.426818 4 1 0 34.0 1.426818 5 0 0 35.0 1.426818 4 0 1 36.0 1.426818 3 1 0 37.0 1.426818 2 1 0 38.0 1.426818 4 0 0 39.0 1.426818 5 0 0 40.0 1.426818 3 1 0 41.0 1.426818 0 0 0 42.0 1.426818 0 0 0 43.0 1.426818 1 0 0 44.0 1.426818 0 0 0 45.0 1.426818 0 0 0 46.0 1.426818 0 0 0 47.0 1.426818 0 0 1 48.0 1.426818 1 0 0 49.0 1.426818 0 0 0 50.0 1.426818 0 0 0 51.0 1.426818 0 0 1 52.0 1.426818 0 0 0 53.0 1.426818 0 0 0 54.0 1.426818 0 0 0 55.0 1.426818 0 0 0 56.0 1.426818 0 0 0 57.0 1.426818 0 0 0 58.0 1.426818 1 0 0 59.0 1.426818 1 0 0 60.0 1.426818 0 0 0 61.0 1.426818 0 0 0 62.0 1.426818 0 0 0 63.0 1.426818 1 0 0 64.0 1.426818 0 0 0 65.0 1.426818 0 0 0 66.0 1.426818 0 0 0 67.0 1.426818 0 0 0 68.0 1.426818 0 0 0 69.0 1.426818 0 0 0 70.0 1.426818 0 0 0 71.0 1.426818 0 0 0 72.0 1.426818 0 0 0 73.0 1.426818 0 0 0 74.0 1.426818 0 0 0 75.0 1.426818 0 0 0 76.0 1.426818 0 0 0 77.0 1.426818 0 0 0 78.0 1.426818 0 0 0 79.0 1.426818 0 0 0 80.0 1.426818 0 0 0 81.0 1.426818 0 0 0 82.0 1.426818 0 0 0 83.0 1.426818 0 0 0 84.0 1.426818 0 0 0 85.0 1.426818 0 0 0 86.0 1.426818 0 0 0 87.0 1.426818 0 0 0 88.0 1.426818 0 0 0 89.0 1.426818 0 0 0 90.0 1.426818 0 0 0 91.0 1.426818 0 0 0 92.0 1.426818 0 0 0 93.0 1.426818 0 0 0 94.0 1.426818 0 0 0 95.0 1.426818 0 0 0 96.0 1.426818 0 0 0 97.0 1.426818 0 0 0 98.0 1.426818 0 0 0 99.0 1.426818 0 0 0 100.0 1.426818 0 0 0