## 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-GSM1606329.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606329.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606329.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 22:36:52 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 37333126 3549132 0 0 4557371 0 0.122073 140197451 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 29758318 29758318 2.0 1.766217 2314841 2314841 3.0 2.353306 417518 417518 4.0 2.803143 135584 135584 5.0 3.147817 59566 59566 6.0 3.411911 30596 30596 7.0 3.614265 17701 17701 8.0 3.769312 10992 10992 9.0 3.888112 7428 7428 10.0 3.979138 5195 5195 11.0 4.048884 3733 3733 12.0 4.102324 2813 2813 13.0 4.143271 2162 2162 14.0 4.174646 1552 1552 15.0 4.198685 1287 1287 16.0 4.217105 956 956 17.0 4.231218 720 720 18.0 4.242032 641 641 19.0 4.250318 540 540 20.0 4.256667 439 439 21.0 4.261531 371 371 22.0 4.265258 353 353 23.0 4.268114 278 278 24.0 4.270302 229 229 25.0 4.271979 181 181 26.0 4.273264 153 153 27.0 4.274248 155 155 28.0 4.275002 130 130 29.0 4.27558 122 122 30.0 4.276023 103 103 31.0 4.276362 91 91 32.0 4.276622 85 85 33.0 4.276822 74 74 34.0 4.276974 66 66 35.0 4.277091 61 61 36.0 4.277181 62 62 37.0 4.277249 42 42 38.0 4.277302 41 41 39.0 4.277342 37 37 40.0 4.277373 28 28 41.0 4.277397 31 31 42.0 4.277415 38 38 43.0 4.277429 36 36 44.0 4.277439 24 24 45.0 4.277448 23 23 46.0 4.277454 17 17 47.0 4.277459 15 15 48.0 4.277462 10 10 49.0 4.277465 11 11 50.0 4.277467 19 19 51.0 4.277469 15 15 52.0 4.27747 16 16 53.0 4.277471 15 15 54.0 4.277472 12 12 55.0 4.277472 8 8 56.0 4.277473 12 12 57.0 4.277473 8 8 58.0 4.277474 6 6 59.0 4.277474 15 15 60.0 4.277474 10 10 61.0 4.277474 5 5 62.0 4.277474 3 3 63.0 4.277474 10 10 64.0 4.277474 4 4 65.0 4.277474 3 3 66.0 4.277474 7 7 67.0 4.277474 9 9 68.0 4.277474 1 1 69.0 4.277474 3 3 70.0 4.277474 5 5 71.0 4.277474 2 2 72.0 4.277474 3 3 73.0 4.277474 4 4 74.0 4.277474 1 1 75.0 4.277474 4 4 76.0 4.277474 5 5 77.0 4.277474 4 4 78.0 4.277474 4 4 79.0 4.277474 2 2 80.0 4.277474 2 2 81.0 4.277474 2 2 82.0 4.277474 0 0 83.0 4.277474 2 2 84.0 4.277474 3 3 85.0 4.277474 1 1 86.0 4.277474 2 2 87.0 4.277474 1 1 88.0 4.277474 1 1 89.0 4.277474 2 2 90.0 4.277474 3 3 91.0 4.277474 3 3 92.0 4.277474 2 2 93.0 4.277474 2 2 94.0 4.277474 0 0 95.0 4.277474 2 2 96.0 4.277474 2 2 97.0 4.277474 1 1 98.0 4.277474 2 2 99.0 4.277474 0 0 100.0 4.277474 2 2 102.0 0 2 2 103.0 0 1 1 108.0 0 2 2 109.0 0 3 3 110.0 0 2 2 113.0 0 1 1 114.0 0 1 1 117.0 0 1 1 119.0 0 1 1 121.0 0 1 1 123.0 0 1 1 127.0 0 1 1 128.0 0 2 2 130.0 0 2 2 131.0 0 1 1 132.0 0 1 1 133.0 0 1 1 135.0 0 1 1 139.0 0 1 1 143.0 0 1 1 152.0 0 1 1 154.0 0 1 1 160.0 0 1 1 164.0 0 1 1 168.0 0 1 1 181.0 0 1 1 186.0 0 1 1 190.0 0 1 1 198.0 0 1 1 209.0 0 1 1 221.0 0 1 1 228.0 0 1 1 244.0 0 1 1 290.0 0 1 1 351.0 0 1 1 404.0 0 1 1 427.0 0 1 1 451.0 0 1 1 577.0 0 1 1 580.0 0 1 1 596.0 0 1 1 672.0 0 1 1 675.0 0 1 1 728.0 0 1 1 744.0 0 1 1 935.0 0 1 1 974.0 0 1 1 1116.0 0 1 1 25248.0 0 1 1