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4 </style><?xml version="1.0" encoding="utf-8" ?>
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5 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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6 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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7 <head>
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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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10 <title></title>
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11 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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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 wrapper run picard_wrapper at 07/05/2011 00:15:30</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="tempSamHead.txt">tempSamHead.txt</a></td></tr>
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17 <tr><td><a href="rgPicardHsMetrics.bait">rgPicardHsMetrics.bait</a></td></tr>
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18 <tr><td><a href="CalculateHsMetrics.metrics.txt">CalculateHsMetrics.metrics.txt</a></td></tr>
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19 </table><p/>
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20 <b>Picard on line resources - maxrows=100</b><ul>
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21 <li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
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22 <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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23 <b>Picard output (transposed to make it easier to see)</b><hr/>
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24 <table cellpadding="3" >
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25 <tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp VALIDATION_STRINGENCY=LENIENT 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>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sat May 07 00:15:15 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.directed.HsMetrics</td></tr><tr class="d0"><td>BAIT_SET</td><td>rgPicardHsMetrics</td></tr>
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26 <tr class="d1"><td>GENOME_SIZE</td><td>2040</td></tr>
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27 <tr class="d0"><td>BAIT_TERRITORY</td><td>14601938</td></tr>
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28 <tr class="d1"><td>TARGET_TERRITORY</td><td>14601938</td></tr>
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29 <tr class="d0"><td>BAIT_DESIGN_EFFICIENCY</td><td>1</td></tr>
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30 <tr class="d1"><td>TOTAL_READS</td><td>18</td></tr>
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31 <tr class="d0"><td>PF_READS</td><td>16</td></tr>
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32 <tr class="d1"><td>PF_UNIQUE_READS</td><td>16</td></tr>
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33 <tr class="d0"><td>PCT_PF_READS</td><td>0.888889</td></tr>
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34 <tr class="d1"><td>PCT_PF_UQ_READS</td><td>0.888889</td></tr>
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35 <tr class="d0"><td>PF_UQ_READS_ALIGNED</td><td>10</td></tr>
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36 <tr class="d1"><td>PCT_PF_UQ_READS_ALIGNED</td><td>0.625</td></tr>
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37 <tr class="d0"><td>PF_UQ_BASES_ALIGNED</td><td>1010</td></tr>
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38 <tr class="d1"><td>ON_BAIT_BASES</td><td>0</td></tr>
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39 <tr class="d0"><td>NEAR_BAIT_BASES</td><td>0</td></tr>
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40 <tr class="d1"><td>OFF_BAIT_BASES</td><td>1010</td></tr>
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41 <tr class="d0"><td>ON_TARGET_BASES</td><td>0</td></tr>
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42 <tr class="d1"><td>PCT_SELECTED_BASES</td><td>0</td></tr>
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43 <tr class="d0"><td>PCT_OFF_BAIT</td><td>1</td></tr>
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44 <tr class="d1"><td>ON_BAIT_VS_SELECTED</td><td>?</td></tr>
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45 <tr class="d0"><td>MEAN_BAIT_COVERAGE</td><td>0</td></tr>
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46 <tr class="d1"><td>MEAN_TARGET_COVERAGE</td><td>?</td></tr>
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47 <tr class="d0"><td>PCT_USABLE_BASES_ON_BAIT</td><td>0</td></tr>
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48 <tr class="d1"><td>PCT_USABLE_BASES_ON_TARGET</td><td>0</td></tr>
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49 <tr class="d0"><td>FOLD_ENRICHMENT</td><td>0</td></tr>
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50 <tr class="d1"><td>ZERO_CVG_TARGETS_PCT</td><td>0.841776</td></tr>
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51 <tr class="d0"><td>FOLD_80_BASE_PENALTY</td><td>?</td></tr>
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52 <tr class="d1"><td>PCT_TARGET_BASES_2X</td><td>0</td></tr>
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53 <tr class="d0"><td>PCT_TARGET_BASES_10X</td><td>0</td></tr>
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54 <tr class="d1"><td>PCT_TARGET_BASES_20X</td><td>0</td></tr>
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55 <tr class="d0"><td>PCT_TARGET_BASES_30X</td><td>0</td></tr>
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56 <tr class="d1"><td>HS_LIBRARY_SIZE</td><td></td></tr>
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57 <tr class="d0"><td>HS_PENALTY_10X</td><td>0</td></tr>
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58 <tr class="d1"><td>HS_PENALTY_20X</td><td>0</td></tr>
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59 <tr class="d0"><td>HS_PENALTY_30X
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60 </td><td>0
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61 </td></tr>
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62 </table>
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63 <b>Picard log</b><hr/>
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64 <pre>## got 10 rows of header
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65 ## executing java -Xmx8G -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CalculateHsMetrics.jar VALIDATION_STRINGENCY=LENIENT BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp returned status 0 and stderr:
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66 [Sat May 07 00:15:15 EDT 2011] net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
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67 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8307873-8307942
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68 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8309830-8309966
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69 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8321581-8321736
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70 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8328921-8329047
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71 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8330342-8330469
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72 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331089-8331268
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73 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331692-8331978
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74 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8365935-8366090
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75 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8366606-8366726
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76 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8379231-8379407
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77 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8394536-8394660
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78 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8426591-8426689
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79 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8439724-8439837
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80 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8450410-8450571
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81 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8455465-8455675
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82 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8460994-8461085
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83 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8474118-8474378
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84 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475226-8475324
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85 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475761-8476349
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86 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8482861-8482979
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87 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8487241-8487268
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88 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8489646-8489840
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89 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8490753-8491059
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90 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8494260-8494405
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91 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8497300-8497434
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92 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8507847-8508429
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93 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8511276-8511546
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94 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8513512-8513524
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95 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8514924-8515035
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96 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8516626-8516644
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97 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8517344-8517353
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98 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8518590-8518779
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99 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8623316-8623458
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100 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8626698-8626844
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101 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8723779-8723843
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102 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8307873-8307942
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103 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8309830-8309966
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104 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8321581-8321736
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105 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8328921-8329047
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106 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8330342-8330469
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107 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331089-8331268
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108 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8331692-8331978
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109 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8365935-8366090
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110 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8366606-8366726
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111 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8379231-8379407
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112 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8394536-8394660
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113 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8426591-8426689
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114 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8439724-8439837
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115 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8450410-8450571
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116 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8455465-8455675
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117 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8460994-8461085
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118 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8474118-8474378
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119 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475226-8475324
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120 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8475761-8476349
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121 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8482861-8482979
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122 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8487241-8487268
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123 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8489646-8489840
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124 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8490753-8491059
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125 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8494260-8494405
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126 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8497300-8497434
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127 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8507847-8508429
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128 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8511276-8511546
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129 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8514924-8515035
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130 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8518590-8518779
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131 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8623316-8623458
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132 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8626698-8626844
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133 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:8723779-8723843
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134 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16408986-16409647
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135 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16425552-16427522
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136 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16542527-16542763
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137 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16572980-16573083
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138 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16717794-16717995
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139 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16728357-16728483
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140 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:16860643-16860646
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141 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125814448-125814568
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142 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125816060-125816263
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143 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125817221-125817625
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144 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125823198-125823404
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145 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:125834519-125834807
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146 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2019022-2019247
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147 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2022951-2023081
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148 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2029465-2029900
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149 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2037228-2037484
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150 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2044596-2044723
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151 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2046671-2046845
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152 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2048290-2048464
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153 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2050815-2050986
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154 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2060417-2060471
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155 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2063211-2063342
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156 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2063565-2063623
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157 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2066228-2066329
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158 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2067628-2067776
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159 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2071831-2071995
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160 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2073346-2073413
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161 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2074085-2074196
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162 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2076828-2077071
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163 WARNING 2011-05-07 00:15:16 IntervalList Ignoring interval for unknown reference: chr9:2078499-2078613
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164
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165 <b>## WARNING - 434559 log lines truncated - CalculateHsMetrics.log contains entire output</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
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166 generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
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167
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