## 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-GSM1606331.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606331.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606331.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 14:24:03 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 24780764 2983972 0 0 2472278 0 0.099766 115788983 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 20635241 20635241 2.0 1.807335 1307092 1307092 3.0 2.459125 218689 218689 4.0 2.985337 70295 70295 5.0 3.410167 30735 30735 6.0 3.753147 15825 15825 7.0 4.030047 9232 9232 8.0 4.253598 5835 5835 9.0 4.434079 3776 3776 10.0 4.579787 2704 2704 11.0 4.697422 1823 1823 12.0 4.792393 1417 1417 13.0 4.869067 1027 1027 14.0 4.930968 814 814 15.0 4.980943 621 621 16.0 5.021289 487 487 17.0 5.053863 424 424 18.0 5.08016 350 350 19.0 5.101391 285 285 20.0 5.118531 239 239 21.0 5.13237 183 183 22.0 5.143541 175 175 23.0 5.152561 134 134 24.0 5.159843 117 117 25.0 5.165722 101 101 26.0 5.170468 83 83 27.0 5.1743 85 85 28.0 5.177393 59 59 29.0 5.179891 58 58 30.0 5.181907 44 44 31.0 5.183535 42 42 32.0 5.184849 42 42 33.0 5.18591 31 31 34.0 5.186767 33 33 35.0 5.187458 25 25 36.0 5.188016 26 26 37.0 5.188467 18 18 38.0 5.188831 26 26 39.0 5.189125 17 17 40.0 5.189362 18 18 41.0 5.189554 13 13 42.0 5.189708 15 15 43.0 5.189833 21 21 44.0 5.189934 16 16 45.0 5.190015 11 11 46.0 5.190081 11 11 47.0 5.190134 5 5 48.0 5.190177 11 11 49.0 5.190211 7 7 50.0 5.190239 5 5 51.0 5.190262 10 10 52.0 5.19028 6 6 53.0 5.190294 6 6 54.0 5.190306 10 10 55.0 5.190316 2 2 56.0 5.190324 4 4 57.0 5.19033 5 5 58.0 5.190335 3 3 59.0 5.190339 2 2 60.0 5.190342 2 2 61.0 5.190345 1 1 62.0 5.190347 4 4 63.0 5.190349 3 3 64.0 5.19035 4 4 65.0 5.190351 2 2 66.0 5.190352 2 2 67.0 5.190353 3 3 68.0 5.190353 0 0 69.0 5.190354 2 2 70.0 5.190354 2 2 71.0 5.190355 4 4 72.0 5.190355 3 3 73.0 5.190355 2 2 74.0 5.190355 0 0 75.0 5.190355 3 3 76.0 5.190355 2 2 77.0 5.190356 4 4 78.0 5.190356 2 2 79.0 5.190356 0 0 80.0 5.190356 1 1 81.0 5.190356 1 1 82.0 5.190356 1 1 83.0 5.190356 2 2 84.0 5.190356 1 1 85.0 5.190356 0 0 86.0 5.190356 0 0 87.0 5.190356 1 1 88.0 5.190356 3 3 89.0 5.190356 0 0 90.0 5.190356 1 1 91.0 5.190356 1 1 92.0 5.190356 0 0 93.0 5.190356 1 1 94.0 5.190356 1 1 95.0 5.190356 3 3 96.0 5.190356 0 0 97.0 5.190356 0 0 98.0 5.190356 1 1 99.0 5.190356 0 0 100.0 5.190356 0 0 101.0 0 1 1 105.0 0 1 1 109.0 0 2 2 110.0 0 2 2 114.0 0 2 2 115.0 0 1 1 118.0 0 1 1 122.0 0 2 2 145.0 0 1 1 177.0 0 1 1 191.0 0 1 1 197.0 0 1 1 204.0 0 1 1 245.0 0 1 1 250.0 0 1 1 275.0 0 1 1 295.0 0 1 1 308.0 0 1 1 312.0 0 2 2 328.0 0 1 1 379.0 0 1 1 416.0 0 1 1 437.0 0 1 1 438.0 0 1 1 556.0 0 1 1 770.0 0 1 1 15672.0 0 1 1