|
4
|
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 rgEstLibComplexity.py tool output - see http://g2.trac.bx.psu.edu/" />
|
|
|
10 <title></title>
|
|
|
11 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
|
|
|
12 </head>
|
|
|
13 <body>
|
|
|
14 <div class="document">
|
|
|
15 <b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output rgEstLibComplexity.py run at 10/04/2011 14:52:24</b><b>Your job produced the following output files.</b><hr/>
|
|
|
16 <table>
|
|
|
17 <tr><td><a href="estlibcompout.txt">estlibcompout.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 (transposed to make it easier to see)</b><hr/>
|
|
|
23 <table cellpadding="3" >
|
|
|
24 <tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.sam.EstimateLibraryComplexity INPUT=[/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat] OUTPUT=estlibcompout.txt MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 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</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sun Apr 10 14:52:24 EDT 2011</td></tr></table>
|
|
|
25 <b>Picard log</b><hr/>
|
|
|
26 <pre>## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/EstimateLibraryComplexity.jar MIN_IDENTICAL_BASES=5 O=estlibcompout.txt VALIDATION_STRINGENCY=LENIENT MIN_MEAN_QUALITY=20 READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 I=/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat MAX_DIFF_RATE=0.03 returned status 0 and log (stdout/stderr) records:
|
|
|
27 [Sun Apr 10 14:52:24 EDT 2011] net.sf.picard.sam.EstimateLibraryComplexity INPUT=[/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat] OUTPUT=estlibcompout.txt MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 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
|
|
|
28 INFO 2011-04-10 14:52:24 EstimateLibraryComplexity Will store 3098916 read pairs in memory before sorting.
|
|
|
29 INFO 2011-04-10 14:52:24 EstimateLibraryComplexity Finished reading - moving on to scanning for duplicates.
|
|
|
30 [Sun Apr 10 14:52:24 EDT 2011] net.sf.picard.sam.EstimateLibraryComplexity done.
|
|
|
31 Runtime.totalMemory()=33947648
|
|
|
32
|
|
|
33
|
|
|
34 </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
|
|
|
35 generated all outputs reported here, using this command line:<br/>
|
|
|
36 <pre>java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/EstimateLibraryComplexity.jar MIN_IDENTICAL_BASES=5 O=estlibcompout.txt VALIDATION_STRINGENCY=LENIENT MIN_MEAN_QUALITY=20 READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 I=/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat MAX_DIFF_RATE=0.03</pre>
|
|
|
37 </div></body></html>
|
|
|
38
|
