## 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-GSM1606349.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606349.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606349.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: Tue Nov 02 14:00:56 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 26763382 4006726 0 0 4305373 0 0.160868 74000933 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 20154798 20154798 2.0 1.696517 1641502 1641502 3.0 2.181653 333536 333536 4.0 2.519559 127074 127074 5.0 2.754916 63985 63985 6.0 2.918847 37278 37278 7.0 3.033027 23706 23706 8.0 3.112556 16238 16238 9.0 3.167949 11492 11492 10.0 3.206531 8564 8564 11.0 3.233404 6485 6485 12.0 3.252121 5054 5054 13.0 3.265159 3964 3964 14.0 3.274239 3229 3229 15.0 3.280564 2667 2667 16.0 3.284969 2160 2160 17.0 3.288038 1817 1817 18.0 3.290175 1529 1529 19.0 3.291663 1396 1396 20.0 3.2927 1189 1189 21.0 3.293422 1006 1006 22.0 3.293925 885 885 23.0 3.294276 722 722 24.0 3.29452 709 709 25.0 3.29469 580 580 26.0 3.294808 492 492 27.0 3.294891 473 473 28.0 3.294948 414 414 29.0 3.294988 343 343 30.0 3.295016 338 338 31.0 3.295035 273 273 32.0 3.295049 262 262 33.0 3.295058 272 272 34.0 3.295065 236 236 35.0 3.295069 221 221 36.0 3.295073 179 179 37.0 3.295075 180 180 38.0 3.295076 172 172 39.0 3.295077 157 157 40.0 3.295078 138 138 41.0 3.295079 120 120 42.0 3.295079 123 123 43.0 3.295079 117 117 44.0 3.295079 118 118 45.0 3.29508 92 92 46.0 3.29508 78 78 47.0 3.29508 85 85 48.0 3.29508 73 73 49.0 3.29508 51 51 50.0 3.29508 71 71 51.0 3.29508 73 73 52.0 3.29508 49 49 53.0 3.29508 59 59 54.0 3.29508 44 44 55.0 3.29508 47 47 56.0 3.29508 32 32 57.0 3.29508 41 41 58.0 3.29508 46 46 59.0 3.29508 44 44 60.0 3.29508 29 29 61.0 3.29508 29 29 62.0 3.29508 33 33 63.0 3.29508 45 45 64.0 3.29508 35 35 65.0 3.29508 33 33 66.0 3.29508 18 18 67.0 3.29508 36 36 68.0 3.29508 21 21 69.0 3.29508 35 35 70.0 3.29508 27 27 71.0 3.29508 26 26 72.0 3.29508 14 14 73.0 3.29508 25 25 74.0 3.29508 17 17 75.0 3.29508 15 15 76.0 3.29508 6 6 77.0 3.29508 11 11 78.0 3.29508 11 11 79.0 3.29508 15 15 80.0 3.29508 13 13 81.0 3.29508 16 16 82.0 3.29508 17 17 83.0 3.29508 11 11 84.0 3.29508 13 13 85.0 3.29508 7 7 86.0 3.29508 9 9 87.0 3.29508 11 11 88.0 3.29508 11 11 89.0 3.29508 10 10 90.0 3.29508 12 12 91.0 3.29508 12 12 92.0 3.29508 8 8 93.0 3.29508 10 10 94.0 3.29508 7 7 95.0 3.29508 16 16 96.0 3.29508 6 6 97.0 3.29508 4 4 98.0 3.29508 4 4 99.0 3.29508 8 8 100.0 3.29508 10 10 101.0 0 7 7 102.0 0 8 8 103.0 0 7 7 104.0 0 5 5 105.0 0 4 4 106.0 0 3 3 107.0 0 2 2 108.0 0 5 5 109.0 0 3 3 110.0 0 1 1 111.0 0 7 7 112.0 0 4 4 113.0 0 3 3 114.0 0 2 2 115.0 0 7 7 116.0 0 8 8 117.0 0 1 1 118.0 0 3 3 119.0 0 5 5 120.0 0 3 3 121.0 0 2 2 122.0 0 2 2 123.0 0 6 6 124.0 0 3 3 125.0 0 3 3 126.0 0 3 3 127.0 0 5 5 128.0 0 2 2 129.0 0 4 4 130.0 0 2 2 131.0 0 2 2 132.0 0 3 3 133.0 0 2 2 134.0 0 2 2 137.0 0 2 2 138.0 0 3 3 139.0 0 2 2 140.0 0 3 3 141.0 0 4 4 142.0 0 2 2 144.0 0 2 2 146.0 0 1 1 147.0 0 1 1 148.0 0 3 3 150.0 0 3 3 151.0 0 2 2 153.0 0 3 3 156.0 0 2 2 157.0 0 2 2 158.0 0 1 1 159.0 0 1 1 160.0 0 1 1 161.0 0 1 1 162.0 0 1 1 163.0 0 3 3 166.0 0 5 5 167.0 0 2 2 172.0 0 1 1 173.0 0 1 1 174.0 0 1 1 175.0 0 1 1 176.0 0 3 3 177.0 0 1 1 179.0 0 1 1 180.0 0 2 2 181.0 0 1 1 182.0 0 1 1 185.0 0 1 1 189.0 0 1 1 190.0 0 1 1 191.0 0 1 1 193.0 0 1 1 194.0 0 2 2 197.0 0 2 2 199.0 0 2 2 203.0 0 2 2 206.0 0 1 1 209.0 0 1 1 214.0 0 1 1 217.0 0 2 2 218.0 0 1 1 219.0 0 1 1 226.0 0 1 1 229.0 0 1 1 234.0 0 1 1 242.0 0 1 1 244.0 0 1 1 248.0 0 1 1 251.0 0 2 2 258.0 0 1 1 260.0 0 1 1 263.0 0 2 2 267.0 0 1 1 268.0 0 1 1 318.0 0 1 1 326.0 0 1 1 338.0 0 1 1 362.0 0 1 1 367.0 0 1 1 416.0 0 1 1 454.0 0 1 1 474.0 0 1 1 5112.0 0 1 1