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| author | devteam |
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| date | Tue, 23 Oct 2012 10:49:35 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_estlibcomplexity_tinysam.html Tue Oct 23 10:49:35 2012 -0400 @@ -0,0 +1,38 @@ +<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 rgEstLibComplexity.py tool output - see http://g2.trac.bx.psu.edu/" /> +<title></title> +<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> +</head> +<body> +<div class="document"> +<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/> +<table> +<tr><td><a href="estlibcompout.txt">estlibcompout.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 (transposed to make it easier to see)</b><hr/> +<table cellpadding="3" > +<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> +<b>Picard log</b><hr/> +<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: +[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 +INFO 2011-04-10 14:52:24 EstimateLibraryComplexity Will store 3098916 read pairs in memory before sorting. +INFO 2011-04-10 14:52:24 EstimateLibraryComplexity Finished reading - moving on to scanning for duplicates. +[Sun Apr 10 14:52:24 EDT 2011] net.sf.picard.sam.EstimateLibraryComplexity done. +Runtime.totalMemory()=33947648 + + +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here, using this command line:<br/> +<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> +</div></body></html> +