## 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-GSM1606353.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606353.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606353.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 15:01:03 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 20873561 3444484 0 0 2674627 0 0.128135 74334089 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16756176 16756176 2.0 1.755174 1021669 1021669 3.0 2.325461 211817 211817 4.0 2.756127 82530 82530 5.0 3.081355 41163 41163 6.0 3.326959 24029 24029 7.0 3.512432 15019 15019 8.0 3.652496 10361 10361 9.0 3.75827 7238 7238 10.0 3.838147 5342 5342 11.0 3.898468 4087 4087 12.0 3.944021 3049 3049 13.0 3.978421 2532 2532 14.0 4.004399 1944 1944 15.0 4.024017 1590 1590 16.0 4.038832 1269 1269 17.0 4.05002 1099 1099 18.0 4.058469 905 905 19.0 4.064849 750 750 20.0 4.069668 617 617 21.0 4.073306 571 571 22.0 4.076054 506 506 23.0 4.078129 450 450 24.0 4.079696 393 393 25.0 4.08088 326 326 26.0 4.081773 279 279 27.0 4.082448 272 272 28.0 4.082958 236 236 29.0 4.083343 207 207 30.0 4.083633 197 197 31.0 4.083853 183 183 32.0 4.084019 155 155 33.0 4.084144 130 130 34.0 4.084238 137 137 35.0 4.08431 119 119 36.0 4.084364 117 117 37.0 4.084404 87 87 38.0 4.084435 92 92 39.0 4.084458 81 81 40.0 4.084476 69 69 41.0 4.084489 72 72 42.0 4.084499 56 56 43.0 4.084507 45 45 44.0 4.084512 45 45 45.0 4.084517 58 58 46.0 4.08452 39 39 47.0 4.084522 46 46 48.0 4.084524 37 37 49.0 4.084526 35 35 50.0 4.084527 33 33 51.0 4.084527 34 34 52.0 4.084528 37 37 53.0 4.084528 27 27 54.0 4.084529 24 24 55.0 4.084529 22 22 56.0 4.084529 21 21 57.0 4.084529 31 31 58.0 4.084529 16 16 59.0 4.08453 19 19 60.0 4.08453 19 19 61.0 4.08453 23 23 62.0 4.08453 18 18 63.0 4.08453 15 15 64.0 4.08453 15 15 65.0 4.08453 13 13 66.0 4.08453 16 16 67.0 4.08453 20 20 68.0 4.08453 13 13 69.0 4.08453 7 7 70.0 4.08453 14 14 71.0 4.08453 6 6 72.0 4.08453 11 11 73.0 4.08453 5 5 74.0 4.08453 6 6 75.0 4.08453 10 10 76.0 4.08453 9 9 77.0 4.08453 9 9 78.0 4.08453 5 5 79.0 4.08453 8 8 80.0 4.08453 7 7 81.0 4.08453 3 3 82.0 4.08453 8 8 83.0 4.08453 4 4 84.0 4.08453 9 9 85.0 4.08453 2 2 86.0 4.08453 4 4 87.0 4.08453 4 4 88.0 4.08453 6 6 89.0 4.08453 6 6 90.0 4.08453 8 8 91.0 4.08453 5 5 92.0 4.08453 6 6 93.0 4.08453 2 2 94.0 4.08453 3 3 95.0 4.08453 4 4 96.0 4.08453 0 0 97.0 4.08453 4 4 98.0 4.08453 1 1 99.0 4.08453 3 3 100.0 4.08453 5 5 101.0 0 3 3 102.0 0 3 3 103.0 0 3 3 104.0 0 5 5 105.0 0 2 2 106.0 0 3 3 107.0 0 2 2 109.0 0 2 2 110.0 0 2 2 111.0 0 1 1 112.0 0 4 4 113.0 0 3 3 114.0 0 3 3 115.0 0 2 2 116.0 0 3 3 117.0 0 1 1 118.0 0 2 2 119.0 0 2 2 121.0 0 3 3 123.0 0 1 1 125.0 0 1 1 126.0 0 1 1 127.0 0 1 1 129.0 0 2 2 131.0 0 1 1 132.0 0 3 3 133.0 0 1 1 134.0 0 2 2 135.0 0 1 1 136.0 0 2 2 140.0 0 1 1 142.0 0 2 2 143.0 0 1 1 145.0 0 1 1 146.0 0 1 1 147.0 0 3 3 150.0 0 1 1 151.0 0 1 1 153.0 0 1 1 158.0 0 1 1 159.0 0 2 2 162.0 0 1 1 165.0 0 1 1 169.0 0 1 1 170.0 0 1 1 172.0 0 1 1 173.0 0 1 1 178.0 0 1 1 179.0 0 1 1 183.0 0 1 1 188.0 0 1 1 189.0 0 1 1 192.0 0 1 1 201.0 0 2 2 206.0 0 1 1 211.0 0 1 1 228.0 0 1 1 238.0 0 1 1 239.0 0 1 1 241.0 0 1 1 258.0 0 1 1 266.0 0 1 1 283.0 0 1 1 337.0 0 1 1 365.0 0 1 1 422.0 0 1 1 463.0 0 1 1 5582.0 0 1 1