|
0
|
1 <style type="text/css">
|
|
|
2 tr.d0 td {background-color: oldlace; color: black;}
|
|
|
3 tr.d1 td {background-color: aliceblue; color: black;}
|
|
|
4 </style><?xml version="1.0" encoding="utf-8" ?>
|
|
|
5 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
|
|
|
6 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
|
|
7 <head>
|
|
|
8 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
|
|
9 <meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
|
|
|
10 <title></title>
|
|
|
11 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
|
|
|
12 </head>
|
|
|
13 <body>
|
|
|
14 <div class="document">
|
|
|
15 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>
|
|
|
16 <tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr>
|
|
|
17 <tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr>
|
|
|
18 </table><p/>
|
|
|
19 <b>Picard on line resources</b><ul>
|
|
|
20 <li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
|
|
|
21 <li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
|
|
|
22 <b>Picard output</b><hr/>
|
|
|
23 <table cellpadding="3" >
|
|
|
24 <tr class="d0"><td colspan="2">chr1 length= 101 Aligned= 0 Unaligned= 0</td></tr>
|
|
|
25 <tr class="d1"><td colspan="2">chr7 length= 404 Aligned= 7 Unaligned= 0</td></tr>
|
|
|
26 <tr class="d0"><td colspan="2">chr8 length= 202 Aligned= 0 Unaligned= 0</td></tr>
|
|
|
27 <tr class="d1"><td colspan="2">chr10 length= 303 Aligned= 0 Unaligned= 0</td></tr>
|
|
|
28 <tr class="d0"><td colspan="2">chr14 length= 505 Aligned= 0 Unaligned= 0</td></tr>
|
|
|
29 <tr class="d1"><td colspan="2">NoCoordinateCount= 1</td></tr>
|
|
|
30 </table>
|
|
|
31 <b>Picard Tool Run Log</b><hr/>
|
|
|
32 <pre>Thu, 12 May 2011 14:18:22 INFO
|
|
|
33 ## 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:
|
|
|
34 [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
|
|
|
35 [Thu May 12 14:18:22 EDT 2011] net.sf.picard.sam.BamIndexStats done.
|
|
|
36 Runtime.totalMemory()=9109504
|
|
|
37
|
|
|
38
|
|
|
39 </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
|
|
|
40 generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
|
|
|
41
|
