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4 </style><?xml version="1.0" encoding="utf-8" ?>
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8 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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9 <meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
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12 </head>
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13 <body>
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14 <div class="document">
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15 Galaxy tool MarkDuplicates run at 12/05/2011 14:34:29</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
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16 <tr><td><a href="MarkDuplicates.log">MarkDuplicates.log</a></td></tr>
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17 <tr><td><a href="MarkDuplicates.metrics.txt">MarkDuplicates.metrics.txt</a></td></tr>
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18 </table><p/>
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19 <b>Picard on line resources</b><ul>
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20 <li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
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21 <li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
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22 <b>Picard output (transposed to make it easier to see)</b><hr/>
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23 <table cellpadding="3" >
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24 <tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Thu May 12 14:34:28 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.sam.DuplicationMetrics</td></tr><tr class="d0"><td>LIBRARY</td><td> </td></tr>
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25 <tr class="d1"><td>UNPAIRED_READS_EXAMINED</td><td>1 </td></tr>
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26 <tr class="d0"><td>READ_PAIRS_EXAMINED</td><td>3 </td></tr>
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27 <tr class="d1"><td>UNMAPPED_READS</td><td>1 </td></tr>
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28 <tr class="d0"><td>UNPAIRED_READ_DUPLICATES</td><td>1 </td></tr>
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29 <tr class="d1"><td>READ_PAIR_DUPLICATES</td><td>1 </td></tr>
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30 <tr class="d0"><td>READ_PAIR_OPTICAL_DUPLICATES</td><td>0 </td></tr>
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31 <tr class="d1"><td>PERCENT_DUPLICATION</td><td>0.428571 </td></tr>
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32 <tr class="d0"><td>ESTIMATED_LIBRARY_SIZE
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33 </td><td>3
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34 </td></tr>
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35 <tr class="d0"><td colspan="2">## HISTOGRAM java.lang.Double</td></tr><tr class="d0"><td colspan="2">BIN VALUE</td></tr>
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36 <tr class="d1"><td colspan="2">1.0 0.948181</td></tr>
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37 <tr class="d0"><td colspan="2">2.0 1.296997</td></tr>
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38 <tr class="d1"><td colspan="2">3.0 1.425319</td></tr>
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39 <tr class="d0"><td colspan="2">4.0 1.472527</td></tr>
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40 <tr class="d1"><td colspan="2">5.0 1.489893</td></tr>
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41 <tr class="d0"><td colspan="2">6.0 1.496282</td></tr>
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42 <tr class="d1"><td colspan="2">7.0 1.498632</td></tr>
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43 <tr class="d0"><td colspan="2">8.0 1.499497</td></tr>
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44 <tr class="d1"><td colspan="2">9.0 1.499815</td></tr>
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45 <tr class="d0"><td colspan="2">10.0 1.499932</td></tr>
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46 <tr class="d1"><td colspan="2">11.0 1.499975</td></tr>
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47 <tr class="d0"><td colspan="2">12.0 1.499991</td></tr>
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48 <tr class="d1"><td colspan="2">13.0 1.499997</td></tr>
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49 <tr class="d0"><td colspan="2">14.0 1.499999</td></tr>
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50 <tr class="d1"><td colspan="2">15.0 1.5</td></tr>
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51 <tr class="d0"><td colspan="2">16.0 1.5</td></tr>
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52 <tr class="d1"><td colspan="2">17.0 1.5</td></tr>
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53 <tr class="d0"><td colspan="2">18.0 1.5</td></tr>
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54 <tr class="d1"><td colspan="2">19.0 1.5</td></tr>
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55 <tr class="d0"><td colspan="2">20.0 1.5</td></tr>
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56 <tr class="d1"><td colspan="2">21.0 1.5</td></tr>
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57 <tr class="d0"><td colspan="2">22.0 1.5</td></tr>
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58 <tr class="d1"><td colspan="2">23.0 1.5</td></tr>
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59 <tr class="d0"><td colspan="2">24.0 1.5</td></tr>
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60 <tr class="d1"><td colspan="2">25.0 1.5</td></tr>
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61 <tr class="d0"><td colspan="2">26.0 1.5</td></tr>
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62 <tr class="d1"><td colspan="2">27.0 1.5</td></tr>
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63 <tr class="d0"><td colspan="2">28.0 1.5</td></tr>
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64 <tr class="d1"><td colspan="2">29.0 1.5</td></tr>
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65 <tr class="d0"><td colspan="2">30.0 1.5</td></tr>
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66 <tr class="d1"><td colspan="2">31.0 1.5</td></tr>
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67 <tr class="d0"><td colspan="2">32.0 1.5</td></tr>
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68 <tr class="d1"><td colspan="2">33.0 1.5</td></tr>
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69 <tr class="d0"><td colspan="2">34.0 1.5</td></tr>
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70 <tr class="d1"><td colspan="2">35.0 1.5</td></tr>
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71 <tr class="d0"><td colspan="2">36.0 1.5</td></tr>
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72 <tr class="d1"><td colspan="2">37.0 1.5</td></tr>
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73 <tr class="d0"><td colspan="2">38.0 1.5</td></tr>
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74 <tr class="d1"><td colspan="2">39.0 1.5</td></tr>
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75 <tr class="d0"><td colspan="2">40.0 1.5</td></tr>
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76 <tr class="d1"><td colspan="2">41.0 1.5</td></tr>
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77 <tr class="d0"><td colspan="2">42.0 1.5</td></tr>
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78 <tr class="d1"><td colspan="2">43.0 1.5</td></tr>
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79 <tr class="d0"><td colspan="2">44.0 1.5</td></tr>
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80 <tr class="d1"><td colspan="2">45.0 1.5</td></tr>
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81 <tr class="d0"><td colspan="2">46.0 1.5</td></tr>
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82 <tr class="d1"><td colspan="2">47.0 1.5</td></tr>
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83 <tr class="d0"><td colspan="2">48.0 1.5</td></tr>
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84 <tr class="d1"><td colspan="2">49.0 1.5</td></tr>
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85 <tr class="d0"><td colspan="2">50.0 1.5</td></tr>
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86 <tr class="d1"><td colspan="2">51.0 1.5</td></tr>
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87 <tr class="d0"><td colspan="2">52.0 1.5</td></tr>
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88 <tr class="d1"><td colspan="2">53.0 1.5</td></tr>
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89 <tr class="d0"><td colspan="2">54.0 1.5</td></tr>
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90 <tr class="d1"><td colspan="2">55.0 1.5</td></tr>
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91 <tr class="d0"><td colspan="2">56.0 1.5</td></tr>
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92 <tr class="d1"><td colspan="2">57.0 1.5</td></tr>
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93 <tr class="d0"><td colspan="2">58.0 1.5</td></tr>
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94 <tr class="d1"><td colspan="2">59.0 1.5</td></tr>
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95 <tr class="d0"><td colspan="2">60.0 1.5</td></tr>
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96 <tr class="d1"><td colspan="2">61.0 1.5</td></tr>
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97 <tr class="d0"><td colspan="2">62.0 1.5</td></tr>
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98 <tr class="d1"><td colspan="2">63.0 1.5</td></tr>
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99 <tr class="d0"><td colspan="2">64.0 1.5</td></tr>
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100 <tr class="d1"><td colspan="2">65.0 1.5</td></tr>
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101 <tr class="d0"><td colspan="2">66.0 1.5</td></tr>
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102 <tr class="d1"><td colspan="2">67.0 1.5</td></tr>
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103 <tr class="d0"><td colspan="2">68.0 1.5</td></tr>
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104 <tr class="d1"><td colspan="2">69.0 1.5</td></tr>
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105 <tr class="d0"><td colspan="2">70.0 1.5</td></tr>
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106 <tr class="d1"><td colspan="2">71.0 1.5</td></tr>
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107 <tr class="d0"><td colspan="2">72.0 1.5</td></tr>
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108 <tr class="d1"><td colspan="2">73.0 1.5</td></tr>
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109 <tr class="d0"><td colspan="2">74.0 1.5</td></tr>
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110 <tr class="d1"><td colspan="2">75.0 1.5</td></tr>
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111 <tr class="d0"><td colspan="2">76.0 1.5</td></tr>
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112 <tr class="d1"><td colspan="2">77.0 1.5</td></tr>
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113 <tr class="d0"><td colspan="2">78.0 1.5</td></tr>
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114 <tr class="d1"><td colspan="2">79.0 1.5</td></tr>
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115 <tr class="d0"><td colspan="2">80.0 1.5</td></tr>
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116 <tr class="d1"><td colspan="2">81.0 1.5</td></tr>
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117 <tr class="d0"><td colspan="2">82.0 1.5</td></tr>
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118 <tr class="d1"><td colspan="2">83.0 1.5</td></tr>
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119 <tr class="d0"><td colspan="2">84.0 1.5</td></tr>
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120 <tr class="d1"><td colspan="2">85.0 1.5</td></tr>
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121 <tr class="d0"><td colspan="2">86.0 1.5</td></tr>
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122 <tr class="d1"><td colspan="2">87.0 1.5</td></tr>
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123 <tr class="d0"><td colspan="2">88.0 1.5</td></tr>
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124 <tr class="d1"><td colspan="2">89.0 1.5</td></tr>
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125 <tr class="d0"><td colspan="2">90.0 1.5</td></tr>
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126 <tr class="d1"><td colspan="2">91.0 1.5</td></tr>
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127 <tr class="d0"><td colspan="2">92.0 1.5</td></tr>
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128 <tr class="d1"><td colspan="2">93.0 1.5</td></tr>
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129 <tr class="d0"><td colspan="2">94.0 1.5</td></tr>
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130 <tr class="d1"><td colspan="2">95.0 1.5</td></tr>
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131 <tr class="d0"><td colspan="2">96.0 1.5</td></tr>
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132 <tr class="d1"><td colspan="2">97.0 1.5</td></tr>
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133 <tr class="d0"><td colspan="2">98.0 1.5</td></tr>
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134 <tr class="d1"><td colspan="2">99.0 1.5</td></tr>
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135 </table>
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136 <b>Picard Tool Run Log</b><hr/>
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137 <pre>Thu, 12 May 2011 14:34:29 INFO
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138 ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/MarkDuplicates.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 0 and stderr:
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139 [Thu May 12 14:34:28 EDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
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140 INFO 2011-05-12 14:34:28 MarkDuplicates Start of doWork freeMemory: 8644632; totalMemory: 9109504; maxMemory: 1908932608
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141 INFO 2011-05-12 14:34:28 MarkDuplicates Reading input file and constructing read end information.
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142 INFO 2011-05-12 14:34:28 MarkDuplicates Will retain up to 7575129 data points before spilling to disk.
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143 INFO 2011-05-12 14:34:28 MarkDuplicates Read 7 records. 0 pairs never matched.
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144 INFO 2011-05-12 14:34:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 8316168; totalMemory: 130351104; maxMemory: 1908932608
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145 INFO 2011-05-12 14:34:29 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk.
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146 INFO 2011-05-12 14:34:29 MarkDuplicates Traversing read pair information and detecting duplicates.
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147 INFO 2011-05-12 14:34:29 MarkDuplicates Traversing fragment information and detecting duplicates.
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148 INFO 2011-05-12 14:34:29 MarkDuplicates Sorting list of duplicate records.
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149 INFO 2011-05-12 14:34:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 129615120; totalMemory: 607649792; maxMemory: 1908932608
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150 INFO 2011-05-12 14:34:29 MarkDuplicates Marking 3 records as duplicates.
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151 INFO 2011-05-12 14:34:29 MarkDuplicates Found 0 optical duplicate clusters.
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152 INFO 2011-05-12 14:34:29 MarkDuplicates Before output close freeMemory: 128997520; totalMemory: 607649792; maxMemory: 1908932608
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153 INFO 2011-05-12 14:34:29 MarkDuplicates After output close freeMemory: 128997280; totalMemory: 607649792; maxMemory: 1908932608
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154 [Thu May 12 14:34:29 EDT 2011] net.sf.picard.sam.MarkDuplicates done.
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155 Runtime.totalMemory()=607649792
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156
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157
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158 </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
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159 generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
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