## 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-GSM1606195.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606195.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606195.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: Mon Nov 01 20:23:57 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 19730166 3397330 0 0 2368388 0 0.120039 75464901 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 16003387 16003387 2.0 1.769936 975313 975313 3.0 2.362737 201016 201016 4.0 2.819155 75979 75979 5.0 3.170568 36689 36689 6.0 3.441134 20728 20728 7.0 3.649452 12719 12719 8.0 3.809843 8527 8527 9.0 3.933335 5949 5949 10.0 4.028415 4243 4243 11.0 4.10162 3208 3208 12.0 4.157984 2373 2373 13.0 4.20138 1887 1887 14.0 4.234793 1470 1470 15.0 4.260518 1193 1193 16.0 4.280325 1017 1017 17.0 4.295575 739 739 18.0 4.307317 683 683 19.0 4.316357 566 566 20.0 4.323318 439 439 21.0 4.328677 403 403 22.0 4.332803 347 347 23.0 4.33598 285 285 24.0 4.338426 271 271 25.0 4.340309 216 216 26.0 4.341759 180 180 27.0 4.342875 171 171 28.0 4.343735 162 162 29.0 4.344397 143 143 30.0 4.344906 131 131 31.0 4.345298 120 120 32.0 4.3456 105 105 33.0 4.345833 84 84 34.0 4.346012 62 62 35.0 4.34615 72 72 36.0 4.346256 85 85 37.0 4.346338 52 52 38.0 4.346401 55 55 39.0 4.346449 58 58 40.0 4.346486 45 45 41.0 4.346515 30 30 42.0 4.346537 31 31 43.0 4.346554 42 42 44.0 4.346567 43 43 45.0 4.346578 28 28 46.0 4.346585 25 25 47.0 4.346591 24 24 48.0 4.346596 27 27 49.0 4.346599 27 27 50.0 4.346602 18 18 51.0 4.346604 14 14 52.0 4.346606 18 18 53.0 4.346607 20 20 54.0 4.346608 16 16 55.0 4.346609 11 11 56.0 4.346609 8 8 57.0 4.34661 8 8 58.0 4.34661 13 13 59.0 4.34661 9 9 60.0 4.346611 7 7 61.0 4.346611 8 8 62.0 4.346611 5 5 63.0 4.346611 7 7 64.0 4.346611 5 5 65.0 4.346611 9 9 66.0 4.346611 3 3 67.0 4.346611 4 4 68.0 4.346611 11 11 69.0 4.346611 5 5 70.0 4.346611 6 6 71.0 4.346611 10 10 72.0 4.346611 7 7 73.0 4.346611 2 2 74.0 4.346611 6 6 75.0 4.346611 7 7 76.0 4.346611 3 3 77.0 4.346611 2 2 78.0 4.346611 5 5 79.0 4.346611 2 2 80.0 4.346611 2 2 81.0 4.346611 3 3 82.0 4.346611 3 3 83.0 4.346611 2 2 84.0 4.346611 4 4 85.0 4.346611 2 2 86.0 4.346611 0 0 87.0 4.346611 4 4 88.0 4.346611 3 3 89.0 4.346611 1 1 90.0 4.346611 2 2 91.0 4.346611 0 0 92.0 4.346611 3 3 93.0 4.346611 0 0 94.0 4.346611 0 0 95.0 4.346611 3 3 96.0 4.346611 2 2 97.0 4.346611 2 2 98.0 4.346611 2 2 99.0 4.346611 1 1 100.0 4.346611 0 0 101.0 0 1 1 102.0 0 3 3 103.0 0 2 2 104.0 0 1 1 105.0 0 2 2 107.0 0 2 2 108.0 0 1 1 109.0 0 1 1 113.0 0 1 1 114.0 0 1 1 116.0 0 1 1 118.0 0 2 2 120.0 0 1 1 125.0 0 1 1 129.0 0 1 1 130.0 0 2 2 133.0 0 1 1 145.0 0 1 1 149.0 0 1 1 154.0 0 1 1 156.0 0 2 2 160.0 0 1 1 167.0 0 1 1 176.0 0 1 1 177.0 0 1 1 181.0 0 1 1 196.0 0 3 3 240.0 0 1 1 243.0 0 1 1 291.0 0 1 1 2053.0 0 1 1