## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_10/ALK_10_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_10/ALK_10_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/ALK_10/ALK_10_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 117390 55665103 15987950 157314 88245 28530407 640265 0.512789 33739486 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.004576 14397312 0 14488335 2.0 1.197533 6052650 323709 6070235 3.0 1.234596 2980326 56718 2971899 4.0 1.241715 1577343 23778 1560876 5.0 1.243082 871572 11233 853335 6.0 1.243345 499408 5457 483772 7.0 1.243396 292993 2995 280436 8.0 1.243405 175298 1611 165580 9.0 1.243407 106640 967 99317 10.0 1.243407 65995 632 60442 11.0 1.243408 41189 393 37158 12.0 1.243408 26112 238 23219 13.0 1.243408 16548 167 14533 14.0 1.243408 10602 134 9131 15.0 1.243408 6951 88 5787 16.0 1.243408 4609 63 3798 17.0 1.243408 2919 53 2374 18.0 1.243408 1965 31 1517 19.0 1.243408 1337 29 1047 20.0 1.243408 882 26 650 21.0 1.243408 618 13 418 22.0 1.243408 427 16 302 23.0 1.243408 299 9 197 24.0 1.243408 184 13 109 25.0 1.243408 149 4 70 26.0 1.243408 73 7 43 27.0 1.243408 73 3 30 28.0 1.243408 52 2 24 29.0 1.243408 38 2 18 30.0 1.243408 24 2 8 31.0 1.243408 21 3 11 32.0 1.243408 10 1 5 33.0 1.243408 11 2 1 34.0 1.243408 13 3 3 35.0 1.243408 5 3 0 36.0 1.243408 6 0 0 37.0 1.243408 8 0 2 38.0 1.243408 6 0 2 39.0 1.243408 4 0 2 40.0 1.243408 7 0 2 41.0 1.243408 2 1 2 42.0 1.243408 0 0 0 43.0 1.243408 0 0 0 44.0 1.243408 2 0 0 45.0 1.243408 2 0 1 46.0 1.243408 2 0 0 47.0 1.243408 1 0 1 48.0 1.243408 1 0 0 49.0 1.243408 1 0 0 50.0 1.243408 0 0 0 51.0 1.243408 1 0 0 52.0 1.243408 0 0 0 53.0 1.243408 0 0 0 54.0 1.243408 0 0 0 55.0 1.243408 1 0 0 56.0 1.243408 0 0 0 57.0 1.243408 0 0 0 58.0 1.243408 0 0 0 59.0 1.243408 0 0 0 60.0 1.243408 0 0 0 61.0 1.243408 0 0 0 62.0 1.243408 0 0 0 63.0 1.243408 0 0 0 64.0 1.243408 0 0 0 65.0 1.243408 0 0 0 66.0 1.243408 0 0 0 67.0 1.243408 0 0 0 68.0 1.243408 0 0 0 69.0 1.243408 0 0 0 70.0 1.243408 0 0 0 71.0 1.243408 0 0 0 72.0 1.243408 0 0 0 73.0 1.243408 0 0 0 74.0 1.243408 0 0 0 75.0 1.243408 0 0 0 76.0 1.243408 0 0 0 77.0 1.243408 0 0 0 78.0 1.243408 0 0 0 79.0 1.243408 0 0 0 80.0 1.243408 0 0 0 81.0 1.243408 0 0 0 82.0 1.243408 0 0 0 83.0 1.243408 0 0 0 84.0 1.243408 0 0 0 85.0 1.243408 0 0 0 86.0 1.243408 0 0 0 87.0 1.243408 0 0 0 88.0 1.243408 0 0 0 89.0 1.243408 0 0 0 90.0 1.243408 0 0 0 91.0 1.243408 0 0 0 92.0 1.243408 0 0 0 93.0 1.243408 0 0 0 94.0 1.243408 0 0 0 95.0 1.243408 0 0 0 96.0 1.243408 0 0 0 97.0 1.243408 0 0 0 98.0 1.243408 0 0 0 99.0 1.243408 0 0 0 100.0 1.243408 0 0 0 102.0 0 1 0 1 119.0 0 1 0 1 139.0 0 1 0 1 142.0 0 1 0 1