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9 <meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />
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14 <div class="document">
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15 Galaxy tool CollectRnaSeqMetrics run at 26/02/2014 22:17:36</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
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16 <tr><td><a href="CollectRnaSeqMetrics.log">CollectRnaSeqMetrics.log</a></td></tr>
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17 <tr><td><a href="CollectRnaSeqMetrics.metrics.txt">CollectRnaSeqMetrics.metrics.txt</a></td></tr>
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18 </table><p/>
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19 <b>Picard on line resources</b><ul>
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20 <li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
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21 <li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
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22 <b>Picard output (transposed to make it easier to see)</b><hr/>
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23 <table cellpadding="3" >
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24 <tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectRnaSeqMetrics REF_FLAT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/refFlat.txt RIBOSOMAL_INTERVALS=null STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=CollectRnaSeqMetrics.pdf RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/PICARD-in.sam OUTPUT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.metrics.txt ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Wed Feb 26 22:17:31 EST 2014</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.RnaSeqMetrics</td></tr><tr class="d0"><td>PF_BASES</td><td>7321300 </td></tr>
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25 <tr class="d1"><td>PF_ALIGNED_BASES</td><td>7319805 </td></tr>
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26 <tr class="d0"><td>RIBOSOMAL_BASES</td><td> </td></tr>
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27 <tr class="d1"><td>CODING_BASES</td><td>0 </td></tr>
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28 <tr class="d0"><td>UTR_BASES</td><td>0 </td></tr>
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29 <tr class="d1"><td>INTRONIC_BASES</td><td>0 </td></tr>
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30 <tr class="d0"><td>INTERGENIC_BASES</td><td>7319805 </td></tr>
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31 <tr class="d1"><td>IGNORED_READS</td><td>0 </td></tr>
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32 <tr class="d0"><td>CORRECT_STRAND_READS</td><td>0 </td></tr>
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33 <tr class="d1"><td>INCORRECT_STRAND_READS</td><td>0 </td></tr>
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34 <tr class="d0"><td>PCT_RIBOSOMAL_BASES</td><td> </td></tr>
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35 <tr class="d1"><td>PCT_CODING_BASES</td><td>0 </td></tr>
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36 <tr class="d0"><td>PCT_UTR_BASES</td><td>0 </td></tr>
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37 <tr class="d1"><td>PCT_INTRONIC_BASES</td><td>0 </td></tr>
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38 <tr class="d0"><td>PCT_INTERGENIC_BASES</td><td>1 </td></tr>
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39 <tr class="d1"><td>PCT_MRNA_BASES</td><td>0 </td></tr>
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40 <tr class="d0"><td>PCT_USABLE_BASES</td><td>0 </td></tr>
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41 <tr class="d1"><td>PCT_CORRECT_STRAND_READS</td><td>0 </td></tr>
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42 <tr class="d0"><td>MEDIAN_CV_COVERAGE</td><td>0 </td></tr>
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43 <tr class="d1"><td>MEDIAN_5PRIME_BIAS</td><td>0 </td></tr>
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44 <tr class="d0"><td>MEDIAN_3PRIME_BIAS</td><td>0 </td></tr>
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45 <tr class="d1"><td>MEDIAN_5PRIME_TO_3PRIME_BIAS</td><td>0 </td></tr>
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46 <tr class="d0"><td>SAMPLE</td><td> </td></tr>
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47 <tr class="d1"><td>LIBRARY</td><td> </td></tr>
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48 <tr class="d0"><td>READ_GROUP
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49 </td><td>
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50 </td></tr>
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51 </table>
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52 <b>Picard Tool Run Log</b><hr/>
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53 <pre>INFO:root:## executing java -Xmx3000m -Djava.io.tmpdir='/home/dorine/galaxypicard/galaxy-central/database/tmp' -jar /home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/CollectRnaSeqMetrics.jar VALIDATION_STRINGENCY=LENIENT I=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/PICARD-in.sam O=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.metrics.txt CHART_OUTPUT=CollectRnaSeqMetrics.pdf ASSUME_SORTED=true MINIMUM_LENGTH=500 REF_FLAT=/home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/refFlat.txt STRAND_SPECIFICITY=NONE RIBOSOMAL_INTERVALS=null RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=ALL_READS returned status 0 and nothing on stderr
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54
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55 INFO:root:Unable to find expected pdf file /home/dorine/galaxypicard/shed_tools/testtoolshed.g2.bx.psu.edu/repos/devteam/picard1106/c127b3314d53/picard1106/avenir/pourtest/masooortie_files/CollectRnaSeqMetrics.pdf<br/>
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56
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57 </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
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58 generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
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