## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uMTA100nM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uMTA100nM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D12_supernatant_RU1uMTA100nM_2.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/tmp] MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Oct 06 02:55:31 CEST 2023 ## 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 1114 20955267 19939685 0 1032 3723085 0 0.177688 51758829 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 15596788 15596788 2.0 1.667068 1192447 1192447 3.0 2.112047 204144 204144 4.0 2.408879 78407 78407 5.0 2.606885 42243 42243 6.0 2.738969 26435 26435 7.0 2.827078 17674 17674 8.0 2.885853 12582 12582 9.0 2.925059 9482 9482 10.0 2.951213 7125 7125 11.0 2.968659 5609 5609 12.0 2.980297 4585 4585 13.0 2.98806 3747 3747 14.0 2.993238 3130 3130 15.0 2.996693 2600 2600 16.0 2.998997 2257 2257 17.0 3.000534 1884 1884 18.0 3.00156 1657 1657 19.0 3.002244 1505 1505 20.0 3.0027 1253 1253 21.0 3.003005 1149 1149 22.0 3.003208 1003 1003 23.0 3.003343 930 930 24.0 3.003433 809 809 25.0 3.003494 742 742 26.0 3.003534 656 656 27.0 3.003561 640 640 28.0 3.003578 549 549 29.0 3.00359 489 489 30.0 3.003598 479 479 31.0 3.003604 416 416 32.0 3.003607 420 420 33.0 3.00361 378 378 34.0 3.003611 309 309 35.0 3.003612 350 350 36.0 3.003613 329 329 37.0 3.003613 286 286 38.0 3.003614 286 286 39.0 3.003614 257 257 40.0 3.003614 231 231 41.0 3.003614 213 213 42.0 3.003614 203 203 43.0 3.003614 191 191 44.0 3.003614 190 190 45.0 3.003614 150 150 46.0 3.003614 176 176 47.0 3.003614 134 134 48.0 3.003614 163 163 49.0 3.003614 135 135 50.0 3.003614 124 124 51.0 3.003614 134 134 52.0 3.003614 118 118 53.0 3.003614 115 115 54.0 3.003614 86 86 55.0 3.003614 110 110 56.0 3.003614 98 98 57.0 3.003614 79 79 58.0 3.003614 83 83 59.0 3.003614 91 91 60.0 3.003614 73 73 61.0 3.003614 73 73 62.0 3.003614 82 82 63.0 3.003614 62 62 64.0 3.003614 61 61 65.0 3.003614 67 67 66.0 3.003614 59 59 67.0 3.003614 67 67 68.0 3.003614 53 53 69.0 3.003614 57 57 70.0 3.003614 48 48 71.0 3.003614 45 45 72.0 3.003614 52 52 73.0 3.003614 51 51 74.0 3.003614 49 49 75.0 3.003614 57 57 76.0 3.003614 45 45 77.0 3.003614 40 40 78.0 3.003614 57 57 79.0 3.003614 41 41 80.0 3.003614 35 35 81.0 3.003614 39 39 82.0 3.003614 40 40 83.0 3.003614 34 34 84.0 3.003614 41 41 85.0 3.003614 31 31 86.0 3.003614 32 32 87.0 3.003614 39 39 88.0 3.003614 42 42 89.0 3.003614 28 28 90.0 3.003614 31 31 91.0 3.003614 34 34 92.0 3.003614 19 19 93.0 3.003614 30 30 94.0 3.003614 33 33 95.0 3.003614 18 18 96.0 3.003614 22 22 97.0 3.003614 30 30 98.0 3.003614 30 30 99.0 3.003614 27 27 100.0 3.003614 17 17 101.0 0 21 21 102.0 0 31 31 103.0 0 28 28 104.0 0 22 22 105.0 0 20 20 106.0 0 27 27 107.0 0 21 21 108.0 0 20 20 109.0 0 20 20 110.0 0 25 25 111.0 0 12 12 112.0 0 15 15 113.0 0 12 12 114.0 0 19 19 115.0 0 21 21 116.0 0 24 24 117.0 0 14 14 118.0 0 18 18 119.0 0 21 21 120.0 0 18 18 121.0 0 13 13 122.0 0 15 15 123.0 0 9 9 124.0 0 13 13 125.0 0 7 7 126.0 0 9 9 127.0 0 12 12 128.0 0 17 17 129.0 0 16 16 130.0 0 14 14 131.0 0 17 17 132.0 0 16 16 133.0 0 9 9 134.0 0 7 7 135.0 0 14 14 136.0 0 15 15 137.0 0 8 8 138.0 0 16 16 139.0 0 11 11 140.0 0 10 10 141.0 0 11 11 142.0 0 14 14 143.0 0 12 12 144.0 0 9 9 145.0 0 7 7 146.0 0 9 9 147.0 0 7 7 148.0 0 11 11 149.0 0 8 8 150.0 0 10 10 151.0 0 7 7 152.0 0 11 11 153.0 0 11 11 154.0 0 11 11 155.0 0 9 9 156.0 0 7 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