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merged
author Rayan Chikhi <chikhi@psu.edu>
date Mon, 21 Jul 2014 15:25:16 -0400
parents 987dbea3b72f
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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>
<tr><td><a href="CollectRnaSeqMetrics.log">CollectRnaSeqMetrics.log</a></td></tr>
<tr><td><a href="CollectRnaSeqMetrics.metrics.txt">CollectRnaSeqMetrics.metrics.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 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&nbsp;</td></tr>
<tr class="d1"><td>PF_ALIGNED_BASES</td><td>7319805&nbsp;</td></tr>
<tr class="d0"><td>RIBOSOMAL_BASES</td><td>&nbsp;</td></tr>
<tr class="d1"><td>CODING_BASES</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>UTR_BASES</td><td>0&nbsp;</td></tr>
<tr class="d1"><td>INTRONIC_BASES</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>INTERGENIC_BASES</td><td>7319805&nbsp;</td></tr>
<tr class="d1"><td>IGNORED_READS</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>CORRECT_STRAND_READS</td><td>0&nbsp;</td></tr>
<tr class="d1"><td>INCORRECT_STRAND_READS</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>PCT_RIBOSOMAL_BASES</td><td>&nbsp;</td></tr>
<tr class="d1"><td>PCT_CODING_BASES</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>PCT_UTR_BASES</td><td>0&nbsp;</td></tr>
<tr class="d1"><td>PCT_INTRONIC_BASES</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>PCT_INTERGENIC_BASES</td><td>1&nbsp;</td></tr>
<tr class="d1"><td>PCT_MRNA_BASES</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>PCT_USABLE_BASES</td><td>0&nbsp;</td></tr>
<tr class="d1"><td>PCT_CORRECT_STRAND_READS</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>MEDIAN_CV_COVERAGE</td><td>0&nbsp;</td></tr>
<tr class="d1"><td>MEDIAN_5PRIME_BIAS</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>MEDIAN_3PRIME_BIAS</td><td>0&nbsp;</td></tr>
<tr class="d1"><td>MEDIAN_5PRIME_TO_3PRIME_BIAS</td><td>0&nbsp;</td></tr>
<tr class="d0"><td>SAMPLE</td><td>&nbsp;</td></tr>
<tr class="d1"><td>LIBRARY</td><td>&nbsp;</td></tr>
<tr class="d0"><td>READ_GROUP
</td><td>
&nbsp;</td></tr>
</table>
<b>Picard Tool Run Log</b><hr/>
<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

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/>

</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>