## 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-GSM1606188.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606188.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606188.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 14:39:41 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 28382136 3609994 0 0 2662992 0 0.093826 141631671 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 23922777 23922777 2.0 1.818408 1395699 1395699 3.0 2.4882 237646 237646 4.0 3.036364 77056 77056 5.0 3.484985 34148 34148 6.0 3.85214 17575 17575 7.0 4.152624 10276 10276 8.0 4.398541 6466 6466 9.0 4.599802 4268 4268 10.0 4.764516 2985 2985 11.0 4.899319 2083 2083 12.0 5.009643 1630 1630 13.0 5.099933 1181 1181 14.0 5.173828 906 906 15.0 5.234303 739 739 16.0 5.283797 559 559 17.0 5.324303 461 461 18.0 5.357453 401 401 19.0 5.384584 321 321 20.0 5.406788 237 237 21.0 5.42496 185 185 22.0 5.439832 169 169 23.0 5.452003 155 155 24.0 5.461964 151 151 25.0 5.470117 106 106 26.0 5.476789 110 110 27.0 5.482249 75 75 28.0 5.486718 95 95 29.0 5.490375 78 78 30.0 5.493368 61 61 31.0 5.495818 56 56 32.0 5.497823 43 43 33.0 5.499463 43 43 34.0 5.500806 32 32 35.0 5.501905 34 34 36.0 5.502804 25 25 37.0 5.503541 16 16 38.0 5.504143 22 22 39.0 5.504636 16 16 40.0 5.505039 13 13 41.0 5.50537 16 16 42.0 5.50564 13 13 43.0 5.505861 12 12 44.0 5.506042 19 19 45.0 5.50619 8 8 46.0 5.506311 7 7 47.0 5.506411 9 9 48.0 5.506492 13 13 49.0 5.506558 2 2 50.0 5.506613 11 11 51.0 5.506657 7 7 52.0 5.506694 7 7 53.0 5.506724 4 4 54.0 5.506748 7 7 55.0 5.506768 9 9 56.0 5.506784 5 5 57.0 5.506798 6 6 58.0 5.506809 4 4 59.0 5.506818 3 3 60.0 5.506825 1 1 61.0 5.506831 3 3 62.0 5.506836 4 4 63.0 5.50684 3 3 64.0 5.506843 4 4 65.0 5.506846 3 3 66.0 5.506848 4 4 67.0 5.50685 2 2 68.0 5.506851 3 3 69.0 5.506852 2 2 70.0 5.506853 0 0 71.0 5.506854 2 2 72.0 5.506855 1 1 73.0 5.506855 1 1 74.0 5.506856 1 1 75.0 5.506856 2 2 76.0 5.506857 1 1 77.0 5.506857 2 2 78.0 5.506857 1 1 79.0 5.506857 2 2 80.0 5.506857 0 0 81.0 5.506857 1 1 82.0 5.506857 0 0 83.0 5.506858 0 0 84.0 5.506858 1 1 85.0 5.506858 1 1 86.0 5.506858 0 0 87.0 5.506858 2 2 88.0 5.506858 0 0 89.0 5.506858 1 1 90.0 5.506858 0 0 91.0 5.506858 0 0 92.0 5.506858 0 0 93.0 5.506858 1 1 94.0 5.506858 0 0 95.0 5.506858 0 0 96.0 5.506858 2 2 97.0 5.506858 1 1 98.0 5.506858 0 0 99.0 5.506858 3 3 100.0 5.506858 1 1 117.0 0 1 1 119.0 0 1 1 122.0 0 1 1 124.0 0 1 1 137.0 0 1 1 139.0 0 1 1 141.0 0 1 1 143.0 0 1 1 151.0 0 1 1 154.0 0 1 1 155.0 0 1 1 156.0 0 2 2 159.0 0 1 1 160.0 0 1 1 170.0 0 1 1 171.0 0 1 1 180.0 0 1 1 190.0 0 1 1 226.0 0 1 1 250.0 0 1 1 273.0 0 1 1 370.0 0 1 1 391.0 0 1 1 453.0 0 1 1 522.0 0 1 1 5657.0 0 1 1