/test-data/picard_output_insertsize_tinysam.html

https://bitbucket.org/cistrome/cistrome-harvard/ · HTML · 53 lines · 48 code · 5 blank · 0 comment · 0 complexity · aed13e5e89b928014c3f1684ad31737d MD5 · raw file

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  15. Galaxy tool CollectInsertSizeMetrics run at 13/05/2011 15:20:46</b><br/><table cellpadding="10"><tr><td>
  16. <a href="InsertSizeHist.pdf"><img src="InsertSizeHist.jpg" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a>
  17. </tr></td></table>
  18. <b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
  19. <tr><td><a href="CollectInsertSizeMetrics.metrics.txt">CollectInsertSizeMetrics.metrics.txt</a></td></tr>
  20. <tr><td><a href="CollectInsertSizeMetrics.log">CollectInsertSizeMetrics.log</a></td></tr>
  21. <tr><td><a href="InsertSizeHist.pdf">InsertSizeHist.pdf</a></td></tr>
  22. <tr><td><a href="InsertSizeHist.jpg">InsertSizeHist.jpg</a></td></tr>
  23. </table><p/>
  24. <b>Picard on line resources</b><ul>
  25. <li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
  26. <li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
  27. <b>Picard output (transposed to make it easier to see)</b><hr/>
  28. <table cellpadding="3" >
  29. <tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true STOP_AFTER=0 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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri May 13 15:20:45 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.InsertSizeMetrics</td></tr><tr class="d1"><td colspan="2">## HISTOGRAM java.lang.Integer</td></tr><tr class="d0"><td colspan="2">MEDIAN_INSERT_SIZE MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT</td></tr>
  30. <tr class="d1"><td colspan="2">96 96 96 96 ? 1 FR 1 1 1 1 1 1 1 1 1 1</td></tr>
  31. <tr class="d0"><td colspan="2">201 201 201 201 ? 1 RF 1 1 1 1 1 1 1 1 1 1</td></tr>
  32. <tr class="d1"><td colspan="2">insert_size fr_count rf_count</td></tr>
  33. <tr class="d0"><td colspan="2">96 1 0</td></tr>
  34. <tr class="d1"><td colspan="2">201 0 1</td></tr>
  35. </table>
  36. <b>Picard Tool Run Log</b><hr/>
  37. <pre>INFO:root:## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CollectInsertSizeMetrics.jar VALIDATION_STRINGENCY=LENIENT I=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat O=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 returned status 0 and stderr:
  38. [Fri May 13 15:20:45 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true STOP_AFTER=0 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
  39. WARNING 2011-05-13 15:20:45 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway.
  40. INFO 2011-05-13 15:20:46 ProcessExecutor [1] "FR = red" "RF = blue"
  41. INFO 2011-05-13 15:20:46 ProcessExecutor null device
  42. INFO 2011-05-13 15:20:46 ProcessExecutor 1
  43. [Fri May 13 15:20:46 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics done.
  44. Runtime.totalMemory()=9109504
  45. INFO:root:## executing mogrify -format jpg -resize x400 /udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/InsertSizeHist.pdf returned status 0 and nothing on stderr
  46. INFO:root:## executing mogrify -format jpg -resize x400 /udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/InsertSizeHist.pdf returned status 0 and nothing on stderr
  47. </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a>
  48. generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>