## 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-GSM919922.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919922.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919922.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 15:50:15 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 9279687 1350610 0 0 716727 0 0.077236 56938717 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 8064338 8064338 2.0 1.849611 402307 402307 3.0 2.57145 58362 58362 4.0 3.184732 17915 17915 5.0 3.705783 7606 7606 6.0 4.148474 4000 4000 7.0 4.524589 2332 2332 8.0 4.84414 1517 1517 9.0 5.115634 1009 1009 10.0 5.346299 680 680 11.0 5.542274 500 500 12.0 5.708777 412 412 13.0 5.850239 311 311 14.0 5.970427 245 245 15.0 6.07254 186 186 16.0 6.159297 146 146 17.0 6.233006 139 139 18.0 6.29563 106 106 19.0 6.348836 83 83 20.0 6.394041 75 75 21.0 6.432447 66 66 22.0 6.465077 52 52 23.0 6.4928 35 35 24.0 6.516354 49 49 25.0 6.536366 36 36 26.0 6.553368 40 40 27.0 6.567813 36 36 28.0 6.580086 27 27 29.0 6.590513 19 19 30.0 6.599372 22 22 31.0 6.606899 26 26 32.0 6.613293 15 15 33.0 6.618726 12 12 34.0 6.623342 21 21 35.0 6.627264 17 17 36.0 6.630596 14 14 37.0 6.633427 13 13 38.0 6.635832 8 8 39.0 6.637876 6 6 40.0 6.639612 11 11 41.0 6.641087 5 5 42.0 6.64234 7 7 43.0 6.643405 6 6 44.0 6.644309 7 7 45.0 6.645078 3 3 46.0 6.645731 2 2 47.0 6.646286 7 7 48.0 6.646757 9 9 49.0 6.647158 5 5 50.0 6.647498 2 2 51.0 6.647787 3 3 52.0 6.648032 3 3 53.0 6.648241 5 5 54.0 6.648418 4 4 55.0 6.648569 4 4 56.0 6.648697 4 4 57.0 6.648806 5 5 58.0 6.648898 2 2 59.0 6.648977 3 3 60.0 6.649043 4 4 61.0 6.6491 1 1 62.0 6.649148 2 2 63.0 6.649189 0 0 64.0 6.649224 2 2 65.0 6.649253 4 4 66.0 6.649278 1 1 67.0 6.6493 2 2 68.0 6.649318 3 3 69.0 6.649333 1 1 70.0 6.649346 0 0 71.0 6.649357 3 3 72.0 6.649367 2 2 73.0 6.649375 4 4 74.0 6.649381 3 3 75.0 6.649387 1 1 76.0 6.649392 4 4 77.0 6.649396 1 1 78.0 6.6494 2 2 79.0 6.649403 0 0 80.0 6.649405 0 0 81.0 6.649408 1 1 82.0 6.64941 1 1 83.0 6.649411 0 0 84.0 6.649412 0 0 85.0 6.649414 1 1 86.0 6.649415 1 1 87.0 6.649415 1 1 88.0 6.649416 1 1 89.0 6.649417 2 2 90.0 6.649417 1 1 91.0 6.649418 0 0 92.0 6.649418 0 0 93.0 6.649418 1 1 94.0 6.649418 0 0 95.0 6.649419 0 0 96.0 6.649419 1 1 97.0 6.649419 1 1 98.0 6.649419 0 0 99.0 6.649419 1 1 100.0 6.649419 0 0 101.0 0 2 2 104.0 0 1 1 105.0 0 1 1 106.0 0 1 1 107.0 0 1 1 108.0 0 1 1 113.0 0 1 1 116.0 0 1 1 117.0 0 1 1 122.0 0 1 1 123.0 0 2 2 129.0 0 1 1 131.0 0 1 1 136.0 0 1 1 138.0 0 1 1 167.0 0 1 1 173.0 0 1 1 178.0 0 1 1 188.0 0 1 1 194.0 0 1 1 213.0 0 1 1 329.0 0 1 1 385.0 0 1 1 395.0 0 1 1 540.0 0 1 1