## 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-GSM1606216.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606216.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606216.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 23:30:43 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 38755659 6308520 0 0 5694387 0 0.14693 118621929 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 30216467 30216467 2.0 1.721289 1938343 1938343 3.0 2.241546 440769 440769 4.0 2.616802 177305 177305 5.0 2.88747 90749 90749 6.0 3.082699 53356 53356 7.0 3.223516 34445 34445 8.0 3.325086 23273 23273 9.0 3.398347 16838 16838 10.0 3.451189 12189 12189 11.0 3.489304 9476 9476 12.0 3.516795 7066 7066 13.0 3.536625 5840 5840 14.0 3.550927 4712 4712 15.0 3.561244 3734 3734 16.0 3.568685 3201 3201 17.0 3.574052 2706 2706 18.0 3.577923 2225 2225 19.0 3.580716 1876 1876 20.0 3.58273 1632 1632 21.0 3.584183 1424 1424 22.0 3.58523 1224 1224 23.0 3.585986 1028 1028 24.0 3.586531 998 998 25.0 3.586924 862 862 26.0 3.587208 709 709 27.0 3.587413 647 647 28.0 3.58756 596 596 29.0 3.587667 550 550 30.0 3.587743 484 484 31.0 3.587799 417 417 32.0 3.587839 411 411 33.0 3.587868 373 373 34.0 3.587888 336 336 35.0 3.587903 303 303 36.0 3.587914 268 268 37.0 3.587922 270 270 38.0 3.587928 253 253 39.0 3.587932 221 221 40.0 3.587935 209 209 41.0 3.587937 200 200 42.0 3.587938 179 179 43.0 3.587939 179 179 44.0 3.58794 127 127 45.0 3.587941 154 154 46.0 3.587941 131 131 47.0 3.587941 127 127 48.0 3.587942 106 106 49.0 3.587942 100 100 50.0 3.587942 114 114 51.0 3.587942 95 95 52.0 3.587942 93 93 53.0 3.587942 84 84 54.0 3.587942 72 72 55.0 3.587942 92 92 56.0 3.587942 80 80 57.0 3.587942 76 76 58.0 3.587942 64 64 59.0 3.587942 54 54 60.0 3.587942 49 49 61.0 3.587942 47 47 62.0 3.587942 58 58 63.0 3.587942 34 34 64.0 3.587942 41 41 65.0 3.587942 37 37 66.0 3.587942 44 44 67.0 3.587942 40 40 68.0 3.587942 33 33 69.0 3.587942 33 33 70.0 3.587942 25 25 71.0 3.587942 29 29 72.0 3.587942 53 53 73.0 3.587942 27 27 74.0 3.587942 21 21 75.0 3.587942 21 21 76.0 3.587942 34 34 77.0 3.587942 27 27 78.0 3.587942 25 25 79.0 3.587942 31 31 80.0 3.587942 21 21 81.0 3.587942 14 14 82.0 3.587942 18 18 83.0 3.587942 16 16 84.0 3.587942 17 17 85.0 3.587942 22 22 86.0 3.587942 20 20 87.0 3.587942 17 17 88.0 3.587942 17 17 89.0 3.587942 9 9 90.0 3.587942 15 15 91.0 3.587942 11 11 92.0 3.587942 8 8 93.0 3.587942 11 11 94.0 3.587942 11 11 95.0 3.587942 15 15 96.0 3.587942 12 12 97.0 3.587942 6 6 98.0 3.587942 12 12 99.0 3.587942 6 6 100.0 3.587942 8 8 101.0 0 9 9 102.0 0 11 11 103.0 0 12 12 104.0 0 6 6 105.0 0 9 9 106.0 0 8 8 107.0 0 8 8 108.0 0 5 5 109.0 0 3 3 110.0 0 7 7 111.0 0 6 6 112.0 0 3 3 113.0 0 11 11 114.0 0 8 8 115.0 0 7 7 116.0 0 4 4 117.0 0 9 9 118.0 0 7 7 119.0 0 9 9 120.0 0 2 2 121.0 0 3 3 122.0 0 3 3 123.0 0 4 4 124.0 0 1 1 125.0 0 6 6 126.0 0 1 1 127.0 0 9 9 128.0 0 2 2 129.0 0 6 6 130.0 0 2 2 131.0 0 5 5 132.0 0 2 2 133.0 0 5 5 134.0 0 3 3 135.0 0 6 6 136.0 0 1 1 137.0 0 5 5 138.0 0 2 2 139.0 0 6 6 140.0 0 2 2 141.0 0 6 6 143.0 0 3 3 144.0 0 2 2 145.0 0 7 7 146.0 0 1 1 147.0 0 1 1 149.0 0 2 2 150.0 0 1 1 151.0 0 4 4 152.0 0 2 2 155.0 0 1 1 158.0 0 3 3 159.0 0 4 4 160.0 0 1 1 162.0 0 3 3 163.0 0 2 2 164.0 0 3 3 165.0 0 3 3 166.0 0 2 2 167.0 0 1 1 168.0 0 4 4 169.0 0 3 3 170.0 0 1 1 171.0 0 1 1 172.0 0 2 2 174.0 0 1 1 175.0 0 2 2 178.0 0 2 2 179.0 0 1 1 180.0 0 3 3 182.0 0 1 1 183.0 0 1 1 184.0 0 2 2 185.0 0 3 3 187.0 0 2 2 188.0 0 1 1 192.0 0 1 1 193.0 0 2 2 198.0 0 1 1 202.0 0 3 3 203.0 0 1 1 204.0 0 1 1 206.0 0 1 1 207.0 0 1 1 208.0 0 1 1 210.0 0 2 2 212.0 0 1 1 214.0 0 1 1 222.0 0 1 1 223.0 0 1 1 230.0 0 1 1 231.0 0 1 1 233.0 0 1 1 234.0 0 1 1 237.0 0 1 1 238.0 0 1 1 245.0 0 1 1 247.0 0 2 2 251.0 0 1 1 252.0 0 1 1 257.0 0 2 2 258.0 0 1 1 262.0 0 1 1 266.0 0 1 1 267.0 0 1 1 270.0 0 1 1 278.0 0 1 1 282.0 0 1 1 301.0 0 1 1 306.0 0 1 1 307.0 0 1 1 309.0 0 1 1 315.0 0 1 1 317.0 0 1 1 327.0 0 1 1 329.0 0 2 2 334.0 0 2 2 335.0 0 1 1 370.0 0 1 1 404.0 0 1 1 408.0 0 1 1 452.0 0 1 1 463.0 0 1 1 478.0 0 1 1 481.0 0 1 1 504.0 0 1 1 520.0 0 1 1 713.0 0 1 1 799.0 0 1 1 819.0 0 1 1 1506.0 0 1 1 1563.0 0 1 1 11261.0 0 1 1