## 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-GSM1606328.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606328.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606328.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 15:00:16 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 21798121 1835224 0 0 1963823 0 0.090091 113597106 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 18444734 18444734 2.0 1.825398 1111509 1111509 3.0 2.506679 173878 173878 4.0 3.069008 52091 52091 5.0 3.533153 21739 21739 6.0 3.916257 10981 10981 7.0 4.23247 6056 6056 8.0 4.493471 3799 3799 9.0 4.708902 2450 2450 10.0 4.886717 1653 1653 11.0 5.033486 1223 1223 12.0 5.154629 848 848 13.0 5.254619 627 627 14.0 5.337152 450 450 15.0 5.405274 390 390 16.0 5.461501 288 288 17.0 5.507911 227 227 18.0 5.546218 193 193 19.0 5.577837 167 167 20.0 5.603934 125 125 21.0 5.625475 98 98 22.0 5.643255 90 90 23.0 5.657931 73 73 24.0 5.670044 67 67 25.0 5.680042 59 59 26.0 5.688295 52 52 27.0 5.695106 33 33 28.0 5.700729 39 39 29.0 5.705369 36 36 30.0 5.709199 16 16 31.0 5.712361 25 25 32.0 5.714971 21 21 33.0 5.717124 21 21 34.0 5.718902 16 16 35.0 5.72037 12 12 36.0 5.721581 13 13 37.0 5.722581 14 14 38.0 5.723406 8 8 39.0 5.724087 11 11 40.0 5.724649 7 7 41.0 5.725113 12 12 42.0 5.725496 5 5 43.0 5.725812 7 7 44.0 5.726073 6 6 45.0 5.726288 7 7 46.0 5.726466 7 7 47.0 5.726613 4 4 48.0 5.726734 5 5 49.0 5.726834 5 5 50.0 5.726917 2 2 51.0 5.726985 2 2 52.0 5.727041 2 2 53.0 5.727087 2 2 54.0 5.727126 4 4 55.0 5.727157 3 3 56.0 5.727183 4 4 57.0 5.727205 1 1 58.0 5.727223 4 4 59.0 5.727237 0 0 60.0 5.727249 7 7 61.0 5.727259 2 2 62.0 5.727268 1 1 63.0 5.727274 1 1 64.0 5.72728 4 4 65.0 5.727285 1 1 66.0 5.727289 2 2 67.0 5.727292 2 2 68.0 5.727294 0 0 69.0 5.727296 1 1 70.0 5.727298 1 1 71.0 5.7273 4 4 72.0 5.727301 1 1 73.0 5.727302 0 0 74.0 5.727303 1 1 75.0 5.727303 2 2 76.0 5.727304 2 2 77.0 5.727304 2 2 78.0 5.727305 0 0 79.0 5.727305 3 3 80.0 5.727305 0 0 81.0 5.727306 1 1 82.0 5.727306 1 1 83.0 5.727306 1 1 84.0 5.727306 0 0 85.0 5.727306 2 2 86.0 5.727306 2 2 87.0 5.727306 0 0 88.0 5.727306 2 2 89.0 5.727306 0 0 90.0 5.727306 0 0 91.0 5.727306 0 0 92.0 5.727306 0 0 93.0 5.727307 0 0 94.0 5.727307 2 2 95.0 5.727307 0 0 96.0 5.727307 0 0 97.0 5.727307 0 0 98.0 5.727307 1 1 99.0 5.727307 0 0 100.0 5.727307 0 0 103.0 0 1 1 109.0 0 1 1 112.0 0 1 1 113.0 0 1 1 131.0 0 1 1 138.0 0 1 1 145.0 0 1 1 156.0 0 1 1 157.0 0 1 1 174.0 0 1 1 181.0 0 1 1 183.0 0 1 1 199.0 0 1 1 212.0 0 1 1 242.0 0 1 1 299.0 0 1 1 311.0 0 1 1 331.0 0 1 1 339.0 0 1 1 343.0 0 1 1 345.0 0 1 1 372.0 0 1 1 376.0 0 1 1 488.0 0 1 1 590.0 0 1 1 602.0 0 1 1 949.0 0 1 1 18971.0 0 1 1