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author devteam
date Tue, 23 Oct 2012 13:14:29 -0400
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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>
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