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1 <?xml version="1.0" encoding="utf-8" ?>
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2 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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3 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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4 <head>
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5 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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6 <meta name="generator" content="Galaxy rgPicardMarkDups.py tool output - see http://g2.trac.bx.psu.edu/" />
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7 <link rel="stylesheet" href="/static/style/base.css" type="text/css" />
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8 </head>
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9 <body>
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10 <div class="document">
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11 <h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardMarkDups.py run at 19/11/2010 18:25:23</h3>
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12 <b>Your job produced the following outputs - check here for a record of what was done and any unexpected events</b>
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13 <hr />
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14 <div>
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15 <b>Output files.</b>
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16 <table>
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17 <tr><td><a href="rgPicardMarkDups.txt">rgPicardMarkDups.txt (1.8 KB)</a></td></tr>
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18 </table>
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19 </div>
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20 <hr />
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21 <div>
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22 <b>Log of activity</b>
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23 <hr/>
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24 ## executing java -Xmx2g -jar /share/shared/relul.galaxy/tool-data/shared/jars/MarkDuplicates.jar I= /share/shared/relul.galaxy/database/files/000/dataset_57.dat O= /share/shared/relul.galaxy/database/files/000/dataset_99.dat M= rgPicardMarkDupsMetrics.txt READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 1 and log (stdout/stderr) records:
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25 <BR />
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26 [Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates INPUT=/share/shared/relul.galaxy/database/files/000/dataset_57.dat OUTPUT=/share/shared/relul.galaxy/database/files/000/dataset_99.dat METRICS_FILE=rgPicardMarkDupsMetrics.txt READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 REMOVE_DUPLICATES=false ASSUME_SORTED=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 TMP_DIR=/tmp/relul VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
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27 <BR />
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28 INFO 2010-11-19 18:25:23 MarkDuplicates Start of doWork freeMemory: 8645600; totalMemory: 9109504; maxMemory: 1908932608
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29 <BR />
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30 INFO 2010-11-19 18:25:23 MarkDuplicates Reading input file and constructing read end information.
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31 <BR />
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32 INFO 2010-11-19 18:25:23 MarkDuplicates Will retain up to 7575129 data points before spilling to disk.
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33 <BR />
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34 [Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates done.
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35 <BR />
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36 Runtime.totalMemory()=130351104
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37 <BR />
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38 Exception in thread "main" net.sf.picard.PicardException: /share/shared/relul.galaxy/database/files/000/dataset_57.dat is not coordinate sorted.
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39 <BR />
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40 at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:248)
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41 <BR />
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42 at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109)
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43 <BR />
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44 at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165)
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45 <BR />
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46 at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93)
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47 <BR />
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48
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49 <BR />
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50
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51 </div>
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52
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53 <div>
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54 <p>Note: The freely available
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55 <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
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56 generated all outputs reported here. These third party tools were orchestrated by the Galaxy
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57 rgPicardMarkDups.py wrapper and this command line from the Galaxy form:
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58 </p>
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59 <hr />
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60 <div>/share/shared/relul.galaxy/tools/development/rgPicardMarkDups.py -i /share/shared/relul.galaxy/database/files/000/dataset_57.dat -n Dupes Marked --tmp_dir /export/tmp/relul -o /share/shared/relul.galaxy/database/files/000/dataset_99.dat --remdups false --assumesorted true --readregex [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* --optdupedist 100 -j /share/shared/relul.galaxy/tool-data/shared/jars/MarkDuplicates.jar -d /share/shared/relul.galaxy/database/job_working_directory/81/dataset_98_files -t /share/shared/relul.galaxy/database/files/000/dataset_98.dat</div>
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61 </div>
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62 </body>
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63 </html>
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