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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 CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:10</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="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr>
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17 <tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.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.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false 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: Fri Nov 11 08:07:10 EST 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR </td></tr>
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25 <tr class="d1"><td>TOTAL_READS</td><td>4 </td></tr>
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26 <tr class="d0"><td>PF_READS</td><td>4 </td></tr>
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27 <tr class="d1"><td>PCT_PF_READS</td><td>1 </td></tr>
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28 <tr class="d0"><td>PF_NOISE_READS</td><td>0 </td></tr>
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29 <tr class="d1"><td>PF_READS_ALIGNED</td><td>4 </td></tr>
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30 <tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1 </td></tr>
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31 <tr class="d1"><td>PF_ALIGNED_BASES</td><td>404 </td></tr>
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32 <tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>4 </td></tr>
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33 <tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>404 </td></tr>
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34 <tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28 </td></tr>
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35 <tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78 </td></tr>
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36 <tr class="d0"><td>PF_MISMATCH_RATE</td><td>0.777228 </td></tr>
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37 <tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228 </td></tr>
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38 <tr class="d0"><td>PF_INDEL_RATE</td><td>0 </td></tr>
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39 <tr class="d1"><td>MEAN_READ_LENGTH</td><td>101 </td></tr>
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40 <tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>3 </td></tr>
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41 <tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75 </td></tr>
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42 <tr class="d0"><td>BAD_CYCLES</td><td>63 </td></tr>
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43 <tr class="d1"><td>STRAND_BALANCE</td><td>0.25 </td></tr>
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44 <tr class="d0"><td>PCT_CHIMERAS</td><td>0 </td></tr>
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45 <tr class="d1"><td>PCT_ADAPTER</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 -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsfq2hit.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsfq2hit.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and nothing on stderr
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54
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55 INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat returned status 0 and nothing on stderr
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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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