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1 ## htsjdk.samtools.metrics.StringHeader
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2 # org.embl.gbcs.je.jeduplicates.MarkDuplicatesWithMolecularCode MISMATCHES=2 MAX_NUMBER_OF_N=1 BARCODE_FILE=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_5.dat SLOTS=[-1, -2] INPUT=[/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_4.dat] OUTPUT=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_6.dat METRICS_FILE=/var/folders/cf/k7c5rjhj1sggk6x8z1jnw4b80000gp/T/tmp2n_ITx/files/000/dataset_7.dat COMMENT=[test-run] REMOVE_DUPLICATES=true ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT SPLIT_CHAR=: TRIM_HEADERS=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicatesWithMolecularCode COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
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3 ## htsjdk.samtools.metrics.StringHeader
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4 # Started on: Tue Nov 10 17:01:18 CET 2015
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5
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6 ## METRICS CLASS picard.sam.DuplicationMetrics
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7 LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
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8 Unknown Library 196 674 196 186 467 0 0.725389 216
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9
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10 ## HISTOGRAM java.lang.Double
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11 BIN VALUE
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12 1.0 0.997418
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13 2.0 1.041445
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14 3.0 1.043389
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15 4.0 1.043474
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16 5.0 1.043478
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17 6.0 1.043478
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18 7.0 1.043478
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19 8.0 1.043478
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20 9.0 1.043478
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21 10.0 1.043478
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22 11.0 1.043478
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23 12.0 1.043478
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24 13.0 1.043478
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25 14.0 1.043478
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26 15.0 1.043478
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27 16.0 1.043478
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28 17.0 1.043478
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29 18.0 1.043478
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30 19.0 1.043478
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31 20.0 1.043478
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32 21.0 1.043478
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33 22.0 1.043478
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34 23.0 1.043478
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35 24.0 1.043478
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36 25.0 1.043478
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37 26.0 1.043478
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38 27.0 1.043478
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39 28.0 1.043478
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40 29.0 1.043478
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41 30.0 1.043478
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42 31.0 1.043478
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43 32.0 1.043478
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44 33.0 1.043478
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45 34.0 1.043478
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46 35.0 1.043478
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47 36.0 1.043478
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48 37.0 1.043478
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49 38.0 1.043478
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50 39.0 1.043478
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51 40.0 1.043478
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52 41.0 1.043478
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53 42.0 1.043478
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54 43.0 1.043478
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55 44.0 1.043478
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56 45.0 1.043478
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57 46.0 1.043478
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58 47.0 1.043478
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59 48.0 1.043478
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60 49.0 1.043478
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61 50.0 1.043478
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62 51.0 1.043478
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63 52.0 1.043478
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64 53.0 1.043478
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65 54.0 1.043478
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66 55.0 1.043478
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67 56.0 1.043478
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68 57.0 1.043478
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69 58.0 1.043478
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70 59.0 1.043478
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71 60.0 1.043478
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72 61.0 1.043478
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73 62.0 1.043478
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74 63.0 1.043478
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75 64.0 1.043478
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76 65.0 1.043478
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77 66.0 1.043478
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78 67.0 1.043478
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79 68.0 1.043478
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80 69.0 1.043478
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81 70.0 1.043478
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82 71.0 1.043478
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83 72.0 1.043478
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84 73.0 1.043478
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85 74.0 1.043478
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86 75.0 1.043478
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87 76.0 1.043478
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88 77.0 1.043478
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89 78.0 1.043478
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90 79.0 1.043478
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91 80.0 1.043478
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92 81.0 1.043478
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93 82.0 1.043478
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94 83.0 1.043478
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95 84.0 1.043478
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96 85.0 1.043478
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97 86.0 1.043478
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98 87.0 1.043478
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99 88.0 1.043478
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100 89.0 1.043478
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101 90.0 1.043478
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102 91.0 1.043478
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103 92.0 1.043478
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104 93.0 1.043478
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105 94.0 1.043478
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106 95.0 1.043478
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107 96.0 1.043478
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108 97.0 1.043478
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109 98.0 1.043478
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110 99.0 1.043478
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111 100.0 1.043478
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112
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