## 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-GSM1606330.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606330.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606330.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 13:43:21 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 28445411 3096492 0 0 2974826 0 0.10458 126341120 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 23465200 23465200 2.0 1.798398 1554527 1554527 3.0 2.435838 269859 269859 4.0 2.944769 86633 86633 5.0 3.351099 37893 37893 6.0 3.675511 19404 19404 7.0 3.934522 11099 11099 8.0 4.141316 7121 7121 9.0 4.306419 4761 4761 10.0 4.438238 3247 3247 11.0 4.543482 2247 2247 12.0 4.627508 1676 1676 13.0 4.694594 1234 1234 14.0 4.748156 974 974 15.0 4.79092 733 733 16.0 4.825062 604 604 17.0 4.852321 527 527 18.0 4.874085 414 414 19.0 4.891461 340 340 20.0 4.905334 254 254 21.0 4.916411 219 219 22.0 4.925254 203 203 23.0 4.932314 149 149 24.0 4.937951 118 118 25.0 4.942452 114 114 26.0 4.946045 108 108 27.0 4.948914 105 105 28.0 4.951205 86 86 29.0 4.953033 68 68 30.0 4.954493 52 52 31.0 4.955659 49 49 32.0 4.95659 51 51 33.0 4.957333 48 48 34.0 4.957926 38 38 35.0 4.9584 25 25 36.0 4.958778 31 31 37.0 4.95908 21 21 38.0 4.959321 29 29 39.0 4.959513 18 18 40.0 4.959667 16 16 41.0 4.95979 19 19 42.0 4.959888 16 16 43.0 4.959966 15 15 44.0 4.960028 11 11 45.0 4.960078 10 10 46.0 4.960118 9 9 47.0 4.96015 7 7 48.0 4.960175 12 12 49.0 4.960195 7 7 50.0 4.960212 9 9 51.0 4.960224 8 8 52.0 4.960235 10 10 53.0 4.960243 9 9 54.0 4.96025 7 7 55.0 4.960255 5 5 56.0 4.960259 8 8 57.0 4.960262 8 8 58.0 4.960265 3 3 59.0 4.960267 8 8 60.0 4.960269 2 2 61.0 4.96027 3 3 62.0 4.960271 3 3 63.0 4.960272 5 5 64.0 4.960273 5 5 65.0 4.960273 5 5 66.0 4.960274 3 3 67.0 4.960274 7 7 68.0 4.960274 2 2 69.0 4.960275 3 3 70.0 4.960275 4 4 71.0 4.960275 2 2 72.0 4.960275 4 4 73.0 4.960275 0 0 74.0 4.960275 1 1 75.0 4.960275 1 1 76.0 4.960275 3 3 77.0 4.960275 0 0 78.0 4.960275 4 4 79.0 4.960275 1 1 80.0 4.960275 2 2 81.0 4.960275 2 2 82.0 4.960276 3 3 83.0 4.960276 1 1 84.0 4.960276 1 1 85.0 4.960276 2 2 86.0 4.960276 1 1 87.0 4.960276 2 2 88.0 4.960276 1 1 89.0 4.960276 1 1 90.0 4.960276 0 0 91.0 4.960276 2 2 92.0 4.960276 1 1 93.0 4.960276 0 0 94.0 4.960276 0 0 95.0 4.960276 1 1 96.0 4.960276 0 0 97.0 4.960276 2 2 98.0 4.960276 2 2 99.0 4.960276 0 0 100.0 4.960276 0 0 104.0 0 1 1 108.0 0 1 1 111.0 0 1 1 114.0 0 1 1 115.0 0 1 1 118.0 0 1 1 129.0 0 1 1 130.0 0 2 2 132.0 0 1 1 133.0 0 1 1 135.0 0 1 1 140.0 0 1 1 149.0 0 1 1 151.0 0 1 1 154.0 0 1 1 158.0 0 1 1 180.0 0 1 1 185.0 0 1 1 235.0 0 1 1 297.0 0 1 1 343.0 0 1 1 344.0 0 1 1 429.0 0 1 1 491.0 0 1 1 885.0 0 1 1 14678.0 0 1 1