Mercurial > repos > jpruab > jpr_picard

<style type="text/css">
        tr.d0 td {background-color: oldlace; color: black;}
        tr.d1 td {background-color: aliceblue; color: black;}
        </style><?xml version="1.0" encoding="utf-8" ?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
<title></title>
<link rel="stylesheet" href="/static/style/base.css" type="text/css" />
</head>
<body>
<div class="document">
Galaxy tool BamIndexStats run at 12/05/2011 14:18:22</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
<tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr>
<tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr>
</table><p/>
<b>Picard on line resources</b><ul>
<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
<b>Picard output</b><hr/>
<table cellpadding="3" >
<tr class="d0"><td colspan="2">chr1 length=	101	Aligned= 0	Unaligned= 0</td></tr>
<tr class="d1"><td colspan="2">chr7 length=	404	Aligned= 7	Unaligned= 0</td></tr>
<tr class="d0"><td colspan="2">chr8 length=	202	Aligned= 0	Unaligned= 0</td></tr>
<tr class="d1"><td colspan="2">chr10 length=	303	Aligned= 0	Unaligned= 0</td></tr>
<tr class="d0"><td colspan="2">chr14 length=	505	Aligned= 0	Unaligned= 0</td></tr>
<tr class="d1"><td colspan="2">NoCoordinateCount= 1</td></tr>
</table>
<b>Picard Tool Run Log</b><hr/>
<pre>Thu, 12 May 2011 14:18:22 INFO
 ## 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/957/dataset_1017_files/tmpqXGksN.bam returned status 0 and stderr:
[Thu May 12 14:18:21 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/957/dataset_1017_files/tmpqXGksN.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
[Thu May 12 14:18:22 EDT 2011] net.sf.picard.sam.BamIndexStats done.
Runtime.totalMemory()=9109504


</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
author	jpruab
date	Tue, 13 Aug 2013 12:09:14 -0400
parents
children