## 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-GSM1606338.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606338.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606338.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 14:49:15 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 23080249 3234576 0 0 3515456 0 0.152314 67858718 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 17688045 17688045 2.0 1.711683 1305210 1305210 3.0 2.218177 288521 288521 4.0 2.57864 112679 112679 5.0 2.835175 56084 56084 6.0 3.017747 32259 32259 7.0 3.147681 20406 20406 8.0 3.240152 13667 13667 9.0 3.305963 9619 9619 10.0 3.352799 7090 7090 11.0 3.386131 5463 5463 12.0 3.409854 4159 4159 13.0 3.426736 3261 3261 14.0 3.438751 2504 2504 15.0 3.447302 2106 2106 16.0 3.453388 1724 1724 17.0 3.457719 1468 1468 18.0 3.460801 1276 1276 19.0 3.462995 1043 1043 20.0 3.464556 865 865 21.0 3.465667 773 773 22.0 3.466458 630 630 23.0 3.467021 595 595 24.0 3.467421 491 491 25.0 3.467706 473 473 26.0 3.467909 435 435 27.0 3.468053 355 355 28.0 3.468156 281 281 29.0 3.468229 268 268 30.0 3.468281 265 265 31.0 3.468318 215 215 32.0 3.468345 203 203 33.0 3.468363 141 141 34.0 3.468377 151 151 35.0 3.468386 154 154 36.0 3.468393 143 143 37.0 3.468398 125 125 38.0 3.468401 107 107 39.0 3.468404 112 112 40.0 3.468405 89 89 41.0 3.468407 79 79 42.0 3.468408 83 83 43.0 3.468408 55 55 44.0 3.468409 67 67 45.0 3.468409 61 61 46.0 3.468409 52 52 47.0 3.468409 46 46 48.0 3.468409 58 58 49.0 3.46841 42 42 50.0 3.46841 43 43 51.0 3.46841 38 38 52.0 3.46841 37 37 53.0 3.46841 36 36 54.0 3.46841 39 39 55.0 3.46841 31 31 56.0 3.46841 40 40 57.0 3.46841 33 33 58.0 3.46841 24 24 59.0 3.46841 22 22 60.0 3.46841 23 23 61.0 3.46841 14 14 62.0 3.46841 23 23 63.0 3.46841 19 19 64.0 3.46841 27 27 65.0 3.46841 13 13 66.0 3.46841 18 18 67.0 3.46841 14 14 68.0 3.46841 13 13 69.0 3.46841 14 14 70.0 3.46841 12 12 71.0 3.46841 8 8 72.0 3.46841 8 8 73.0 3.46841 7 7 74.0 3.46841 6 6 75.0 3.46841 6 6 76.0 3.46841 6 6 77.0 3.46841 11 11 78.0 3.46841 9 9 79.0 3.46841 5 5 80.0 3.46841 4 4 81.0 3.46841 11 11 82.0 3.46841 9 9 83.0 3.46841 4 4 84.0 3.46841 3 3 85.0 3.46841 1 1 86.0 3.46841 8 8 87.0 3.46841 4 4 88.0 3.46841 5 5 89.0 3.46841 6 6 90.0 3.46841 6 6 91.0 3.46841 1 1 92.0 3.46841 2 2 93.0 3.46841 0 0 94.0 3.46841 8 8 95.0 3.46841 3 3 96.0 3.46841 2 2 97.0 3.46841 6 6 98.0 3.46841 4 4 99.0 3.46841 1 1 100.0 3.46841 6 6 101.0 0 4 4 102.0 0 3 3 103.0 0 4 4 104.0 0 3 3 105.0 0 2 2 106.0 0 2 2 107.0 0 3 3 108.0 0 4 4 109.0 0 4 4 110.0 0 2 2 111.0 0 2 2 112.0 0 3 3 114.0 0 5 5 115.0 0 2 2 116.0 0 3 3 117.0 0 2 2 120.0 0 3 3 122.0 0 3 3 124.0 0 1 1 127.0 0 2 2 128.0 0 1 1 129.0 0 2 2 134.0 0 1 1 135.0 0 1 1 136.0 0 1 1 138.0 0 2 2 140.0 0 1 1 145.0 0 1 1 146.0 0 2 2 149.0 0 1 1 150.0 0 4 4 151.0 0 2 2 155.0 0 1 1 156.0 0 1 1 159.0 0 1 1 161.0 0 1 1 166.0 0 1 1 168.0 0 1 1 171.0 0 2 2 173.0 0 1 1 174.0 0 2 2 176.0 0 1 1 184.0 0 1 1 186.0 0 1 1 190.0 0 1 1 200.0 0 1 1 204.0 0 1 1 210.0 0 1 1 220.0 0 1 1 232.0 0 1 1 243.0 0 1 1 275.0 0 1 1 280.0 0 1 1 321.0 0 1 1 334.0 0 1 1 5892.0 0 1 1