## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1359_21/G1359_21_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1359_21/G1359_21_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1359_21/G1359_21_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: Fri Aug 29 15:41:05 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 20197 29861145 23671455 28607 3010 2103407 0 0.070466 201887599 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 25827599 25827599 2.0 1.862509 1772260 1772260 3.0 2.606431 144141 144141 4.0 3.24807 12319 12319 5.0 3.801489 1251 1251 6.0 4.278818 133 133 7.0 4.690519 22 22 8.0 5.045615 5 5 9.0 5.351888 4 4 10.0 5.616051 1 1 11.0 5.843894 2 2 12.0 6.040411 1 1 13.0 6.209909 0 0 14.0 6.356102 0 0 15.0 6.482195 0 0 16.0 6.590951 0 0 17.0 6.684754 0 0 18.0 6.76566 0 0 19.0 6.835443 0 0 20.0 6.89563 0 0 21.0 6.947543 0 0 22.0 6.992318 0 0 23.0 7.030937 0 0 24.0 7.064246 0 0 25.0 7.092975 0 0 26.0 7.117755 0 0 27.0 7.139127 0 0 28.0 7.157561 0 0 29.0 7.17346 0 0 30.0 7.187174 0 0 31.0 7.199002 0 0 32.0 7.209203 0 0 33.0 7.218003 0 0 34.0 7.225592 0 0 35.0 7.232138 0 0 36.0 7.237783 0 0 37.0 7.242653 0 0 38.0 7.246853 0 0 39.0 7.250476 0 0 40.0 7.2536 0 0 41.0 7.256295 0 0 42.0 7.258619 0 0 43.0 7.260624 0 0 44.0 7.262353 0 0 45.0 7.263845 0 0 46.0 7.265131 0 0 47.0 7.266241 0 0 48.0 7.267198 0 0 49.0 7.268023 0 0 50.0 7.268735 0 0 51.0 7.269349 0 0 52.0 7.269878 0 0 53.0 7.270335 0 0 54.0 7.270729 0 0 55.0 7.271069 0 0 56.0 7.271362 0 0 57.0 7.271615 0 0 58.0 7.271833 0 0 59.0 7.272021 0 0 60.0 7.272183 0 0 61.0 7.272323 0 0 62.0 7.272444 0 0 63.0 7.272548 0 0 64.0 7.272638 0 0 65.0 7.272715 0 0 66.0 7.272782 0 0 67.0 7.272839 0 0 68.0 7.272889 0 0 69.0 7.272932 0 0 70.0 7.272969 0 0 71.0 7.273001 0 0 72.0 7.273028 0 0 73.0 7.273052 0 0 74.0 7.273072 0 0 75.0 7.27309 0 0 76.0 7.273105 0 0 77.0 7.273118 0 0 78.0 7.27313 0 0 79.0 7.273139 0 0 80.0 7.273148 0 0 81.0 7.273155 0 0 82.0 7.273161 0 0 83.0 7.273167 0 0 84.0 7.273171 0 0 85.0 7.273175 0 0 86.0 7.273179 0 0 87.0 7.273182 0 0 88.0 7.273185 0 0 89.0 7.273187 0 0 90.0 7.273189 0 0 91.0 7.27319 0 0 92.0 7.273192 0 0 93.0 7.273193 0 0 94.0 7.273194 0 0 95.0 7.273195 0 0 96.0 7.273196 0 0 97.0 7.273196 0 0 98.0 7.273197 0 0 99.0 7.273198 0 0 100.0 7.273198 0 0