## 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-GSM1606212.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606212.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606212.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 23:32:57 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 39987298 7025636 0 0 6106616 0 0.152714 117223104 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 30854076 30854076 2.0 1.710973 2069234 2069234 3.0 2.216455 465336 465336 4.0 2.575839 185451 185451 5.0 2.831351 95473 95473 6.0 3.013013 56404 56404 7.0 3.14217 35890 35890 8.0 3.233997 24801 24801 9.0 3.299283 17614 17614 10.0 3.3457 13104 13104 11.0 3.378701 9901 9901 12.0 3.402164 7891 7891 13.0 3.418846 6304 6304 14.0 3.430706 5015 5015 15.0 3.439138 4254 4254 16.0 3.445133 3483 3483 17.0 3.449395 2863 2863 18.0 3.452426 2486 2486 19.0 3.45458 2133 2133 20.0 3.456112 1790 1790 21.0 3.457201 1563 1563 22.0 3.457976 1389 1389 23.0 3.458526 1154 1154 24.0 3.458918 1063 1063 25.0 3.459196 915 915 26.0 3.459394 791 791 27.0 3.459534 791 791 28.0 3.459634 679 679 29.0 3.459705 601 601 30.0 3.459756 529 529 31.0 3.459792 555 555 32.0 3.459817 437 437 33.0 3.459836 464 464 34.0 3.459849 391 391 35.0 3.459858 339 339 36.0 3.459864 308 308 37.0 3.459869 293 293 38.0 3.459872 235 235 39.0 3.459875 252 252 40.0 3.459876 221 221 41.0 3.459877 214 214 42.0 3.459878 216 216 43.0 3.459879 169 169 44.0 3.459879 161 161 45.0 3.45988 164 164 46.0 3.45988 176 176 47.0 3.45988 158 158 48.0 3.45988 149 149 49.0 3.45988 124 124 50.0 3.45988 117 117 51.0 3.45988 118 118 52.0 3.45988 87 87 53.0 3.45988 107 107 54.0 3.45988 89 89 55.0 3.45988 92 92 56.0 3.45988 81 81 57.0 3.45988 82 82 58.0 3.45988 67 67 59.0 3.45988 65 65 60.0 3.45988 85 85 61.0 3.45988 50 50 62.0 3.45988 63 63 63.0 3.45988 66 66 64.0 3.45988 63 63 65.0 3.45988 45 45 66.0 3.45988 41 41 67.0 3.45988 43 43 68.0 3.45988 39 39 69.0 3.45988 46 46 70.0 3.45988 45 45 71.0 3.45988 38 38 72.0 3.45988 53 53 73.0 3.45988 34 34 74.0 3.45988 30 30 75.0 3.45988 30 30 76.0 3.45988 35 35 77.0 3.45988 29 29 78.0 3.45988 29 29 79.0 3.45988 21 21 80.0 3.45988 30 30 81.0 3.45988 34 34 82.0 3.45988 22 22 83.0 3.45988 20 20 84.0 3.45988 23 23 85.0 3.45988 23 23 86.0 3.45988 22 22 87.0 3.45988 19 19 88.0 3.45988 21 21 89.0 3.45988 26 26 90.0 3.45988 20 20 91.0 3.45988 10 10 92.0 3.45988 10 10 93.0 3.45988 16 16 94.0 3.45988 12 12 95.0 3.45988 8 8 96.0 3.45988 10 10 97.0 3.45988 13 13 98.0 3.45988 12 12 99.0 3.45988 9 9 100.0 3.45988 11 11 101.0 0 8 8 102.0 0 14 14 103.0 0 12 12 104.0 0 8 8 105.0 0 13 13 106.0 0 14 14 107.0 0 10 10 108.0 0 10 10 109.0 0 13 13 110.0 0 8 8 111.0 0 8 8 112.0 0 9 9 113.0 0 11 11 114.0 0 7 7 115.0 0 6 6 116.0 0 8 8 117.0 0 7 7 118.0 0 9 9 119.0 0 15 15 120.0 0 2 2 121.0 0 8 8 122.0 0 6 6 123.0 0 5 5 124.0 0 7 7 125.0 0 11 11 126.0 0 7 7 127.0 0 5 5 128.0 0 5 5 129.0 0 7 7 130.0 0 7 7 131.0 0 4 4 132.0 0 8 8 133.0 0 5 5 134.0 0 7 7 135.0 0 5 5 136.0 0 4 4 137.0 0 7 7 138.0 0 4 4 139.0 0 2 2 140.0 0 2 2 141.0 0 5 5 142.0 0 3 3 143.0 0 2 2 144.0 0 2 2 145.0 0 5 5 146.0 0 6 6 147.0 0 4 4 148.0 0 3 3 149.0 0 2 2 150.0 0 5 5 151.0 0 5 5 152.0 0 1 1 153.0 0 3 3 154.0 0 3 3 156.0 0 1 1 157.0 0 3 3 158.0 0 1 1 159.0 0 2 2 160.0 0 2 2 161.0 0 3 3 162.0 0 4 4 163.0 0 1 1 164.0 0 1 1 166.0 0 1 1 167.0 0 1 1 169.0 0 1 1 170.0 0 1 1 171.0 0 1 1 173.0 0 3 3 175.0 0 1 1 176.0 0 2 2 178.0 0 5 5 179.0 0 2 2 181.0 0 2 2 182.0 0 1 1 183.0 0 1 1 184.0 0 5 5 185.0 0 2 2 186.0 0 3 3 188.0 0 2 2 189.0 0 2 2 190.0 0 1 1 191.0 0 1 1 193.0 0 1 1 195.0 0 1 1 196.0 0 2 2 197.0 0 2 2 198.0 0 3 3 199.0 0 1 1 200.0 0 1 1 203.0 0 1 1 206.0 0 4 4 207.0 0 1 1 209.0 0 1 1 210.0 0 1 1 211.0 0 3 3 213.0 0 1 1 214.0 0 1 1 215.0 0 1 1 216.0 0 3 3 217.0 0 3 3 219.0 0 1 1 220.0 0 1 1 222.0 0 3 3 225.0 0 1 1 228.0 0 1 1 229.0 0 2 2 230.0 0 2 2 231.0 0 1 1 232.0 0 1 1 233.0 0 2 2 238.0 0 1 1 239.0 0 2 2 241.0 0 1 1 245.0 0 1 1 246.0 0 1 1 248.0 0 2 2 252.0 0 2 2 260.0 0 1 1 264.0 0 1 1 266.0 0 1 1 269.0 0 1 1 270.0 0 1 1 278.0 0 1 1 289.0 0 2 2 293.0 0 1 1 296.0 0 1 1 299.0 0 1 1 300.0 0 1 1 302.0 0 1 1 306.0 0 1 1 313.0 0 1 1 321.0 0 2 2 334.0 0 1 1 337.0 0 1 1 343.0 0 1 1 344.0 0 1 1 346.0 0 1 1 352.0 0 1 1 361.0 0 1 1 364.0 0 1 1 372.0 0 1 1 381.0 0 1 1 400.0 0 1 1 411.0 0 1 1 424.0 0 1 1 437.0 0 1 1 447.0 0 1 1 450.0 0 1 1 463.0 0 2 2 483.0 0 1 1 511.0 0 1 1 541.0 0 1 1 575.0 0 1 1 599.0 0 1 1 619.0 0 1 1 626.0 0 1 1 684.0 0 1 1 735.0 0 1 1 1059.0 0 1 1 1063.0 0 1 1 1162.0 0 1 1 7491.0 0 1 1