## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606219.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606219.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606219.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/siebrenf/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 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Nov 01 22:00:24 CET 2021 ## 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 0 46478905 7155184 0 0 6826208 0 0.146867 142329722 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 36270146 36270146 2.0 1.721403 2281422 2281422 3.0 2.241824 531830 531830 4.0 2.617258 214979 214979 5.0 2.888096 110950 110950 6.0 3.08348 65478 65478 7.0 3.22443 42340 42340 8.0 3.326112 28716 28716 9.0 3.399466 20541 20541 10.0 3.452383 15377 15377 11.0 3.490558 11733 11733 12.0 3.518098 9074 9074 13.0 3.537965 7071 7071 14.0 3.552297 5890 5890 15.0 3.562636 4767 4767 16.0 3.570095 3802 3802 17.0 3.575475 3299 3299 18.0 3.579357 2788 2788 19.0 3.582157 2409 2409 20.0 3.584177 2028 2028 21.0 3.585635 1790 1790 22.0 3.586686 1529 1529 23.0 3.587445 1351 1351 24.0 3.587992 1157 1157 25.0 3.588386 1036 1036 26.0 3.588671 906 906 27.0 3.588876 838 838 28.0 3.589025 730 730 29.0 3.589132 644 644 30.0 3.589209 607 607 31.0 3.589264 507 507 32.0 3.589304 524 524 33.0 3.589333 434 434 34.0 3.589354 385 385 35.0 3.589369 370 370 36.0 3.58938 332 332 37.0 3.589388 275 275 38.0 3.589394 287 287 39.0 3.589398 252 252 40.0 3.589401 231 231 41.0 3.589403 230 230 42.0 3.589404 209 209 43.0 3.589405 191 191 44.0 3.589406 191 191 45.0 3.589407 172 172 46.0 3.589407 154 154 47.0 3.589408 149 149 48.0 3.589408 159 159 49.0 3.589408 116 116 50.0 3.589408 116 116 51.0 3.589408 108 108 52.0 3.589408 100 100 53.0 3.589408 89 89 54.0 3.589408 78 78 55.0 3.589408 58 58 56.0 3.589408 63 63 57.0 3.589408 83 83 58.0 3.589408 67 67 59.0 3.589408 70 70 60.0 3.589408 73 73 61.0 3.589408 61 61 62.0 3.589408 50 50 63.0 3.589408 66 66 64.0 3.589408 46 46 65.0 3.589408 39 39 66.0 3.589408 41 41 67.0 3.589408 42 42 68.0 3.589408 38 38 69.0 3.589408 47 47 70.0 3.589408 37 37 71.0 3.589408 35 35 72.0 3.589408 31 31 73.0 3.589408 36 36 74.0 3.589408 36 36 75.0 3.589408 23 23 76.0 3.589408 27 27 77.0 3.589408 23 23 78.0 3.589408 28 28 79.0 3.589408 21 21 80.0 3.589408 18 18 81.0 3.589408 21 21 82.0 3.589408 21 21 83.0 3.589408 16 16 84.0 3.589408 21 21 85.0 3.589408 13 13 86.0 3.589408 13 13 87.0 3.589408 15 15 88.0 3.589408 26 26 89.0 3.589408 20 20 90.0 3.589408 16 16 91.0 3.589408 20 20 92.0 3.589408 16 16 93.0 3.589408 15 15 94.0 3.589408 17 17 95.0 3.589408 6 6 96.0 3.589408 18 18 97.0 3.589408 15 15 98.0 3.589408 8 8 99.0 3.589408 16 16 100.0 3.589408 7 7 101.0 0 16 16 102.0 0 9 9 103.0 0 9 9 104.0 0 9 9 105.0 0 6 6 106.0 0 5 5 107.0 0 3 3 108.0 0 11 11 109.0 0 6 6 110.0 0 7 7 111.0 0 6 6 112.0 0 3 3 113.0 0 3 3 114.0 0 8 8 115.0 0 5 5 116.0 0 4 4 117.0 0 7 7 118.0 0 7 7 119.0 0 7 7 120.0 0 6 6 121.0 0 4 4 122.0 0 7 7 123.0 0 8 8 124.0 0 2 2 125.0 0 1 1 126.0 0 2 2 127.0 0 3 3 128.0 0 6 6 129.0 0 1 1 130.0 0 4 4 131.0 0 4 4 132.0 0 2 2 133.0 0 2 2 134.0 0 6 6 135.0 0 1 1 136.0 0 3 3 137.0 0 1 1 138.0 0 2 2 139.0 0 3 3 140.0 0 3 3 141.0 0 2 2 142.0 0 4 4 143.0 0 3 3 144.0 0 3 3 145.0 0 2 2 146.0 0 3 3 147.0 0 4 4 148.0 0 1 1 149.0 0 5 5 150.0 0 4 4 151.0 0 5 5 152.0 0 1 1 153.0 0 2 2 154.0 0 2 2 155.0 0 1 1 157.0 0 1 1 158.0 0 2 2 160.0 0 1 1 163.0 0 3 3 165.0 0 1 1 166.0 0 1 1 167.0 0 1 1 168.0 0 2 2 170.0 0 2 2 171.0 0 1 1 172.0 0 2 2 174.0 0 1 1 175.0 0 1 1 176.0 0 2 2 177.0 0 2 2 178.0 0 2 2 181.0 0 3 3 186.0 0 2 2 187.0 0 1 1 190.0 0 3 3 192.0 0 2 2 193.0 0 1 1 196.0 0 2 2 197.0 0 2 2 198.0 0 2 2 200.0 0 2 2 201.0 0 1 1 202.0 0 1 1 205.0 0 1 1 207.0 0 1 1 208.0 0 2 2 209.0 0 1 1 212.0 0 1 1 213.0 0 1 1 215.0 0 1 1 216.0 0 1 1 218.0 0 3 3 219.0 0 1 1 221.0 0 1 1 225.0 0 1 1 227.0 0 1 1 229.0 0 1 1 232.0 0 1 1 235.0 0 1 1 238.0 0 1 1 240.0 0 1 1 242.0 0 2 2 254.0 0 1 1 259.0 0 1 1 276.0 0 1 1 280.0 0 1 1 290.0 0 1 1 291.0 0 1 1 309.0 0 1 1 312.0 0 1 1 317.0 0 1 1 320.0 0 1 1 330.0 0 1 1 340.0 0 1 1 346.0 0 1 1 364.0 0 1 1 378.0 0 1 1 843.0 0 1 1 8674.0 0 1 1