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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 BamIndexStats run at 12/05/2011 14:18:06</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="BamIndexStats.log">BamIndexStats.log</a></td></tr>
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17 <tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.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</b><hr/>
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23 <table cellpadding="3" >
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24 <tr class="d0"><td colspan="2">chr1 length= 101 Aligned= 0 Unaligned= 0</td></tr>
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25 <tr class="d1"><td colspan="2">chr7 length= 404 Aligned= 7 Unaligned= 0</td></tr>
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26 <tr class="d0"><td colspan="2">chr8 length= 202 Aligned= 0 Unaligned= 0</td></tr>
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27 <tr class="d1"><td colspan="2">NoCoordinateCount= 1</td></tr>
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28 </table>
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29 <b>Picard Tool Run Log</b><hr/>
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30 <pre>Thu, 12 May 2011 14:18:06 INFO
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31 ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/galaxy-central/database/job_working_directory/955/dataset_1015_files/tmp45bd_D.bam returned status 0 and stderr:
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32 [Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/955/dataset_1015_files/tmp45bd_D.bam VALIDATION_STRINGENCY=LENIENT 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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33 [Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats done.
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34 Runtime.totalMemory()=9109504
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35
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36
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37 </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
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38 generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
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39
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