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/test-data/picard_BIS_output2.txt

https://bitbucket.org/cistrome/cistrome-harvard/
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15Galaxy 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.
36Runtime.totalMemory()=9109504
37
38
39</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
40generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
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