## 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-GSM1606183.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606183.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606183.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 22:35:41 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 36438826 2715666 0 0 3481783 0 0.095551 178326208 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 30524159 30524159 2.0 1.815187 1913129 1913129 3.0 2.479716 321505 321505 4.0 3.021432 99276 99276 5.0 3.463031 41095 41095 6.0 3.823017 20691 20691 7.0 4.116473 11849 11849 8.0 4.355694 7069 7069 9.0 4.550704 4718 4718 10.0 4.709674 3160 3160 11.0 4.839264 2232 2232 12.0 4.944904 1651 1651 13.0 5.03102 1221 1221 14.0 5.101221 975 975 15.0 5.158448 665 665 16.0 5.205099 593 593 17.0 5.243127 412 412 18.0 5.274128 387 387 19.0 5.299399 278 278 20.0 5.32 264 264 21.0 5.336794 207 207 22.0 5.350484 192 192 23.0 5.361644 139 139 24.0 5.370741 116 116 25.0 5.378157 119 119 26.0 5.384202 114 114 27.0 5.38913 103 103 28.0 5.393148 71 71 29.0 5.396423 77 77 30.0 5.399092 48 48 31.0 5.401269 52 52 32.0 5.403043 44 44 33.0 5.404489 36 36 34.0 5.405668 32 32 35.0 5.406629 25 25 36.0 5.407412 21 21 37.0 5.408051 24 24 38.0 5.408572 16 16 39.0 5.408996 13 13 40.0 5.409342 20 20 41.0 5.409624 20 20 42.0 5.409854 16 16 43.0 5.410041 18 18 44.0 5.410194 7 7 45.0 5.410319 10 10 46.0 5.41042 12 12 47.0 5.410503 5 5 48.0 5.41057 11 11 49.0 5.410625 11 11 50.0 5.41067 5 5 51.0 5.410707 5 5 52.0 5.410737 5 5 53.0 5.410761 5 5 54.0 5.410781 4 4 55.0 5.410797 3 3 56.0 5.41081 6 6 57.0 5.410821 5 5 58.0 5.410829 4 4 59.0 5.410837 2 2 60.0 5.410842 5 5 61.0 5.410847 2 2 62.0 5.410851 3 3 63.0 5.410854 2 2 64.0 5.410857 2 2 65.0 5.410859 4 4 66.0 5.41086 0 0 67.0 5.410862 3 3 68.0 5.410863 2 2 69.0 5.410864 2 2 70.0 5.410865 1 1 71.0 5.410865 1 1 72.0 5.410866 4 4 73.0 5.410866 0 0 74.0 5.410866 0 0 75.0 5.410867 3 3 76.0 5.410867 3 3 77.0 5.410867 0 0 78.0 5.410867 3 3 79.0 5.410867 2 2 80.0 5.410868 0 0 81.0 5.410868 1 1 82.0 5.410868 3 3 83.0 5.410868 1 1 84.0 5.410868 1 1 85.0 5.410868 0 0 86.0 5.410868 0 0 87.0 5.410868 0 0 88.0 5.410868 1 1 89.0 5.410868 1 1 90.0 5.410868 0 0 91.0 5.410868 1 1 92.0 5.410868 5 5 93.0 5.410868 1 1 94.0 5.410868 0 0 95.0 5.410868 0 0 96.0 5.410868 4 4 97.0 5.410868 0 0 98.0 5.410868 0 0 99.0 5.410868 0 0 100.0 5.410868 1 1 102.0 0 1 1 106.0 0 1 1 109.0 0 2 2 111.0 0 3 3 112.0 0 1 1 115.0 0 1 1 127.0 0 1 1 134.0 0 1 1 151.0 0 1 1 152.0 0 1 1 154.0 0 1 1 162.0 0 1 1 194.0 0 1 1 217.0 0 1 1 224.0 0 1 1 226.0 0 1 1 237.0 0 1 1 243.0 0 1 1 330.0 0 1 1 343.0 0 1 1 377.0 0 1 1 503.0 0 1 1 519.0 0 1 1 560.0 0 1 1 627.0 0 1 1 8671.0 0 1 1