## 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-GSM1606265.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606265.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606265.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 15:16:00 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 18766532 3235184 0 0 2777906 0 0.148024 56966590 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 14314699 14314699 2.0 1.719333 1252240 1252240 3.0 2.236774 227814 227814 4.0 2.608986 80413 80413 5.0 2.87673 39037 39037 6.0 3.069328 21786 21786 7.0 3.20787 13328 13328 8.0 3.307527 9147 9147 9.0 3.379215 6418 6418 10.0 3.430781 4647 4647 11.0 3.467875 3444 3444 12.0 3.494558 2549 2549 13.0 3.513752 2060 2060 14.0 3.527559 1659 1659 15.0 3.53749 1347 1347 16.0 3.544635 1104 1104 17.0 3.549774 861 861 18.0 3.55347 749 749 19.0 3.556129 596 596 20.0 3.558042 509 509 21.0 3.559418 448 448 22.0 3.560408 378 378 23.0 3.56112 332 332 24.0 3.561632 278 278 25.0 3.562 244 244 26.0 3.562265 231 231 27.0 3.562456 190 190 28.0 3.562593 185 185 29.0 3.562692 180 180 30.0 3.562763 146 146 31.0 3.562814 142 142 32.0 3.562851 107 107 33.0 3.562877 96 96 34.0 3.562896 90 90 35.0 3.56291 86 86 36.0 3.562919 97 97 37.0 3.562927 73 73 38.0 3.562932 74 74 39.0 3.562935 59 59 40.0 3.562938 40 40 41.0 3.56294 42 42 42.0 3.562941 47 47 43.0 3.562942 48 48 44.0 3.562943 37 37 45.0 3.562943 33 33 46.0 3.562944 35 35 47.0 3.562944 28 28 48.0 3.562944 20 20 49.0 3.562944 30 30 50.0 3.562944 26 26 51.0 3.562945 29 29 52.0 3.562945 22 22 53.0 3.562945 17 17 54.0 3.562945 13 13 55.0 3.562945 16 16 56.0 3.562945 17 17 57.0 3.562945 17 17 58.0 3.562945 14 14 59.0 3.562945 11 11 60.0 3.562945 18 18 61.0 3.562945 6 6 62.0 3.562945 13 13 63.0 3.562945 13 13 64.0 3.562945 7 7 65.0 3.562945 10 10 66.0 3.562945 5 5 67.0 3.562945 8 8 68.0 3.562945 13 13 69.0 3.562945 7 7 70.0 3.562945 5 5 71.0 3.562945 6 6 72.0 3.562945 1 1 73.0 3.562945 4 4 74.0 3.562945 4 4 75.0 3.562945 1 1 76.0 3.562945 1 1 77.0 3.562945 5 5 78.0 3.562945 5 5 79.0 3.562945 8 8 80.0 3.562945 5 5 81.0 3.562945 2 2 82.0 3.562945 1 1 83.0 3.562945 3 3 84.0 3.562945 1 1 85.0 3.562945 4 4 86.0 3.562945 3 3 87.0 3.562945 5 5 88.0 3.562945 3 3 89.0 3.562945 6 6 90.0 3.562945 0 0 91.0 3.562945 3 3 92.0 3.562945 5 5 93.0 3.562945 3 3 94.0 3.562945 4 4 95.0 3.562945 4 4 96.0 3.562945 1 1 97.0 3.562945 1 1 98.0 3.562945 5 5 99.0 3.562945 2 2 100.0 3.562945 2 2 101.0 0 1 1 102.0 0 2 2 103.0 0 1 1 105.0 0 2 2 106.0 0 2 2 107.0 0 1 1 109.0 0 2 2 111.0 0 2 2 112.0 0 3 3 113.0 0 2 2 114.0 0 2 2 115.0 0 2 2 118.0 0 2 2 119.0 0 1 1 123.0 0 2 2 130.0 0 1 1 135.0 0 1 1 142.0 0 1 1 147.0 0 1 1 148.0 0 3 3 158.0 0 1 1 159.0 0 1 1 175.0 0 1 1 2108.0 0 1 1