## 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-GSM1606351.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606351.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606351.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 15:15:00 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 17260391 2689694 0 0 1934335 0 0.112068 71140788 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 14256062 14256062 2.0 1.784567 758412 758412 3.0 2.400113 159913 159913 4.0 2.88305 61136 61136 5.0 3.261947 30347 30347 6.0 3.559216 17269 17269 7.0 3.792445 11074 11074 8.0 3.975428 7311 7311 9.0 4.11899 5101 5101 10.0 4.231625 3775 3775 11.0 4.319994 2713 2713 12.0 4.389326 2122 2122 13.0 4.443721 1649 1649 14.0 4.486398 1341 1341 15.0 4.519881 1085 1085 16.0 4.546151 882 882 17.0 4.566761 765 765 18.0 4.582931 576 576 19.0 4.595618 526 526 20.0 4.605571 483 483 21.0 4.61338 399 399 22.0 4.619507 306 306 23.0 4.624314 263 263 24.0 4.628085 246 246 25.0 4.631044 182 182 26.0 4.633365 181 181 27.0 4.635187 181 181 28.0 4.636616 144 144 29.0 4.637737 130 130 30.0 4.638616 104 104 31.0 4.639306 111 111 32.0 4.639848 93 93 33.0 4.640273 85 85 34.0 4.640606 96 96 35.0 4.640867 81 81 36.0 4.641073 58 58 37.0 4.641234 63 63 38.0 4.64136 59 59 39.0 4.641459 49 49 40.0 4.641537 39 39 41.0 4.641598 44 44 42.0 4.641645 35 35 43.0 4.641683 44 44 44.0 4.641712 32 32 45.0 4.641736 25 25 46.0 4.641754 31 31 47.0 4.641768 30 30 48.0 4.641779 21 21 49.0 4.641788 27 27 50.0 4.641795 17 17 51.0 4.6418 12 12 52.0 4.641804 18 18 53.0 4.641808 16 16 54.0 4.64181 10 10 55.0 4.641812 16 16 56.0 4.641814 16 16 57.0 4.641815 13 13 58.0 4.641816 9 9 59.0 4.641817 11 11 60.0 4.641817 12 12 61.0 4.641818 14 14 62.0 4.641818 8 8 63.0 4.641819 10 10 64.0 4.641819 10 10 65.0 4.641819 9 9 66.0 4.641819 7 7 67.0 4.641819 5 5 68.0 4.641819 9 9 69.0 4.641819 6 6 70.0 4.641819 8 8 71.0 4.64182 7 7 72.0 4.64182 1 1 73.0 4.64182 2 2 74.0 4.64182 4 4 75.0 4.64182 3 3 76.0 4.64182 3 3 77.0 4.64182 3 3 78.0 4.64182 6 6 79.0 4.64182 1 1 80.0 4.64182 3 3 81.0 4.64182 4 4 82.0 4.64182 7 7 83.0 4.64182 4 4 84.0 4.64182 1 1 85.0 4.64182 3 3 86.0 4.64182 3 3 87.0 4.64182 1 1 88.0 4.64182 3 3 89.0 4.64182 2 2 90.0 4.64182 3 3 91.0 4.64182 0 0 92.0 4.64182 2 2 93.0 4.64182 4 4 94.0 4.64182 1 1 95.0 4.64182 0 0 96.0 4.64182 0 0 97.0 4.64182 0 0 98.0 4.64182 3 3 99.0 4.64182 0 0 100.0 4.64182 2 2 101.0 0 2 2 103.0 0 2 2 104.0 0 1 1 105.0 0 1 1 107.0 0 2 2 108.0 0 1 1 109.0 0 2 2 110.0 0 1 1 112.0 0 2 2 113.0 0 1 1 114.0 0 3 3 117.0 0 2 2 119.0 0 4 4 120.0 0 1 1 121.0 0 1 1 123.0 0 2 2 125.0 0 1 1 126.0 0 1 1 127.0 0 1 1 129.0 0 1 1 130.0 0 1 1 132.0 0 1 1 133.0 0 1 1 137.0 0 1 1 155.0 0 1 1 156.0 0 1 1 213.0 0 1 1 214.0 0 1 1 229.0 0 1 1 253.0 0 1 1 3392.0 0 1 1