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/test-data/picard_output_markdups_sortedpairsam.html

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  14. <div class="document">
    15. 

  15. Galaxy tool MarkDuplicates run at 12/05/2011 14:34:29</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>
    16. 

  16. <tr><td><a href="MarkDuplicates.log">MarkDuplicates.log</a></td></tr>
    17. 

  17. <tr><td><a href="MarkDuplicates.metrics.txt">MarkDuplicates.metrics.txt</a></td></tr>
    18. 

  18. </table><p/>
    19. 

  19. <b>Picard on line resources</b><ul>
    20. 

  20. <li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>
    21. 

  21. <li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>
    22. 

  22. <b>Picard output (transposed to make it easier to see)</b><hr/>
    23. 

  23. <table cellpadding="3" >
    24. 

  24. <tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 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: Thu May 12 14:34:28 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS	net.sf.picard.sam.DuplicationMetrics</td></tr><tr class="d0"><td>LIBRARY</td><td>&nbsp;</td></tr>
    25. 

  25. <tr class="d1"><td>UNPAIRED_READS_EXAMINED</td><td>1&nbsp;</td></tr>
    26. 

  26. <tr class="d0"><td>READ_PAIRS_EXAMINED</td><td>3&nbsp;</td></tr>
    27. 

  27. <tr class="d1"><td>UNMAPPED_READS</td><td>1&nbsp;</td></tr>
    28. 

  28. <tr class="d0"><td>UNPAIRED_READ_DUPLICATES</td><td>1&nbsp;</td></tr>
    29. 

  29. <tr class="d1"><td>READ_PAIR_DUPLICATES</td><td>1&nbsp;</td></tr>
    30. 

  30. <tr class="d0"><td>READ_PAIR_OPTICAL_DUPLICATES</td><td>0&nbsp;</td></tr>
    31. 

  31. <tr class="d1"><td>PERCENT_DUPLICATION</td><td>0.428571&nbsp;</td></tr>
    32. 

  32. <tr class="d0"><td>ESTIMATED_LIBRARY_SIZE
    33. 

  33. </td><td>3
    34. 

  34. &nbsp;</td></tr>
    35. 

  35. <tr class="d0"><td colspan="2">## HISTOGRAM	java.lang.Double</td></tr><tr class="d0"><td colspan="2">BIN	VALUE</td></tr>
    36. 

  36. <tr class="d1"><td colspan="2">1.0	0.948181</td></tr>
    37. 

  37. <tr class="d0"><td colspan="2">2.0	1.296997</td></tr>
    38. 

  38. <tr class="d1"><td colspan="2">3.0	1.425319</td></tr>
    39. 

  39. <tr class="d0"><td colspan="2">4.0	1.472527</td></tr>
    40. 

  40. <tr class="d1"><td colspan="2">5.0	1.489893</td></tr>
    41. 

  41. <tr class="d0"><td colspan="2">6.0	1.496282</td></tr>
    42. 

  42. <tr class="d1"><td colspan="2">7.0	1.498632</td></tr>
    43. 

  43. <tr class="d0"><td colspan="2">8.0	1.499497</td></tr>
    44. 

  44. <tr class="d1"><td colspan="2">9.0	1.499815</td></tr>
    45. 

  45. <tr class="d0"><td colspan="2">10.0	1.499932</td></tr>
    46. 

  46. <tr class="d1"><td colspan="2">11.0	1.499975</td></tr>
    47. 

  47. <tr class="d0"><td colspan="2">12.0	1.499991</td></tr>
    48. 

  48. <tr class="d1"><td colspan="2">13.0	1.499997</td></tr>
    49. 

  49. <tr class="d0"><td colspan="2">14.0	1.499999</td></tr>
    50. 

  50. <tr class="d1"><td colspan="2">15.0	1.5</td></tr>
    51. 

  51. <tr class="d0"><td colspan="2">16.0	1.5</td></tr>
    52. 

  52. <tr class="d1"><td colspan="2">17.0	1.5</td></tr>
    53. 

  53. <tr class="d0"><td colspan="2">18.0	1.5</td></tr>
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  54. <tr class="d1"><td colspan="2">19.0	1.5</td></tr>
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  55. <tr class="d0"><td colspan="2">20.0	1.5</td></tr>
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  56. <tr class="d1"><td colspan="2">21.0	1.5</td></tr>
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  57. <tr class="d0"><td colspan="2">22.0	1.5</td></tr>
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  58. <tr class="d1"><td colspan="2">23.0	1.5</td></tr>
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  59. <tr class="d0"><td colspan="2">24.0	1.5</td></tr>
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  60. <tr class="d1"><td colspan="2">25.0	1.5</td></tr>
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  61. <tr class="d0"><td colspan="2">26.0	1.5</td></tr>
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  62. <tr class="d1"><td colspan="2">27.0	1.5</td></tr>
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  63. <tr class="d0"><td colspan="2">28.0	1.5</td></tr>
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  64. <tr class="d1"><td colspan="2">29.0	1.5</td></tr>
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  65. <tr class="d0"><td colspan="2">30.0	1.5</td></tr>
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  66. <tr class="d1"><td colspan="2">31.0	1.5</td></tr>
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  67. <tr class="d0"><td colspan="2">32.0	1.5</td></tr>
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  68. <tr class="d1"><td colspan="2">33.0	1.5</td></tr>
    69. 

  69. <tr class="d0"><td colspan="2">34.0	1.5</td></tr>
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  70. <tr class="d1"><td colspan="2">35.0	1.5</td></tr>
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  71. <tr class="d0"><td colspan="2">36.0	1.5</td></tr>
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  72. <tr class="d1"><td colspan="2">37.0	1.5</td></tr>
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  73. <tr class="d0"><td colspan="2">38.0	1.5</td></tr>
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  74. <tr class="d1"><td colspan="2">39.0	1.5</td></tr>
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  75. <tr class="d0"><td colspan="2">40.0	1.5</td></tr>
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  76. <tr class="d1"><td colspan="2">41.0	1.5</td></tr>
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  77. <tr class="d0"><td colspan="2">42.0	1.5</td></tr>
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  78. <tr class="d1"><td colspan="2">43.0	1.5</td></tr>
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  79. <tr class="d0"><td colspan="2">44.0	1.5</td></tr>
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  80. <tr class="d1"><td colspan="2">45.0	1.5</td></tr>
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  81. <tr class="d0"><td colspan="2">46.0	1.5</td></tr>
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  82. <tr class="d1"><td colspan="2">47.0	1.5</td></tr>
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  83. <tr class="d0"><td colspan="2">48.0	1.5</td></tr>
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  84. <tr class="d1"><td colspan="2">49.0	1.5</td></tr>
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  85. <tr class="d0"><td colspan="2">50.0	1.5</td></tr>
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  86. <tr class="d1"><td colspan="2">51.0	1.5</td></tr>
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  87. <tr class="d0"><td colspan="2">52.0	1.5</td></tr>
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  88. <tr class="d1"><td colspan="2">53.0	1.5</td></tr>
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  89. <tr class="d0"><td colspan="2">54.0	1.5</td></tr>
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  90. <tr class="d1"><td colspan="2">55.0	1.5</td></tr>
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  91. <tr class="d0"><td colspan="2">56.0	1.5</td></tr>
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  92. <tr class="d1"><td colspan="2">57.0	1.5</td></tr>
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  93. <tr class="d0"><td colspan="2">58.0	1.5</td></tr>
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  94. <tr class="d1"><td colspan="2">59.0	1.5</td></tr>
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  95. <tr class="d0"><td colspan="2">60.0	1.5</td></tr>
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  96. <tr class="d1"><td colspan="2">61.0	1.5</td></tr>
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  97. <tr class="d0"><td colspan="2">62.0	1.5</td></tr>
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  98. <tr class="d1"><td colspan="2">63.0	1.5</td></tr>
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  99. <tr class="d0"><td colspan="2">64.0	1.5</td></tr>
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  100. <tr class="d1"><td colspan="2">65.0	1.5</td></tr>
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  101. <tr class="d0"><td colspan="2">66.0	1.5</td></tr>
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  102. <tr class="d1"><td colspan="2">67.0	1.5</td></tr>
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  103. <tr class="d0"><td colspan="2">68.0	1.5</td></tr>
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  104. <tr class="d1"><td colspan="2">69.0	1.5</td></tr>
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  105. <tr class="d0"><td colspan="2">70.0	1.5</td></tr>
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  106. <tr class="d1"><td colspan="2">71.0	1.5</td></tr>
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  107. <tr class="d0"><td colspan="2">72.0	1.5</td></tr>
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  108. <tr class="d1"><td colspan="2">73.0	1.5</td></tr>
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  109. <tr class="d0"><td colspan="2">74.0	1.5</td></tr>
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  110. <tr class="d1"><td colspan="2">75.0	1.5</td></tr>
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  111. <tr class="d0"><td colspan="2">76.0	1.5</td></tr>
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  112. <tr class="d1"><td colspan="2">77.0	1.5</td></tr>
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  113. <tr class="d0"><td colspan="2">78.0	1.5</td></tr>
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  114. <tr class="d1"><td colspan="2">79.0	1.5</td></tr>
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  115. <tr class="d0"><td colspan="2">80.0	1.5</td></tr>
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  116. <tr class="d1"><td colspan="2">81.0	1.5</td></tr>
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  117. <tr class="d0"><td colspan="2">82.0	1.5</td></tr>
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  118. <tr class="d1"><td colspan="2">83.0	1.5</td></tr>
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  119. <tr class="d0"><td colspan="2">84.0	1.5</td></tr>
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  120. <tr class="d1"><td colspan="2">85.0	1.5</td></tr>
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  121. <tr class="d0"><td colspan="2">86.0	1.5</td></tr>
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  122. <tr class="d1"><td colspan="2">87.0	1.5</td></tr>
    123. 

  123. <tr class="d0"><td colspan="2">88.0	1.5</td></tr>
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  124. <tr class="d1"><td colspan="2">89.0	1.5</td></tr>
    125. 

  125. <tr class="d0"><td colspan="2">90.0	1.5</td></tr>
    126. 

  126. <tr class="d1"><td colspan="2">91.0	1.5</td></tr>
    127. 

  127. <tr class="d0"><td colspan="2">92.0	1.5</td></tr>
    128. 

  128. <tr class="d1"><td colspan="2">93.0	1.5</td></tr>
    129. 

  129. <tr class="d0"><td colspan="2">94.0	1.5</td></tr>
    130. 

  130. <tr class="d1"><td colspan="2">95.0	1.5</td></tr>
    131. 

  131. <tr class="d0"><td colspan="2">96.0	1.5</td></tr>
    132. 

  132. <tr class="d1"><td colspan="2">97.0	1.5</td></tr>
    133. 

  133. <tr class="d0"><td colspan="2">98.0	1.5</td></tr>
    134. 

  134. <tr class="d1"><td colspan="2">99.0	1.5</td></tr>
    135. 

  135. </table>
    136. 

  136. <b>Picard Tool Run Log</b><hr/>
    137. 

  137. <pre>Thu, 12 May 2011 14:34:29 INFO
    138. 

  138.  ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/MarkDuplicates.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 0 and stderr: 
    139. 

  139. [Thu May 12 14:34:28 EDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
    140. 

  140. INFO	2011-05-12 14:34:28	MarkDuplicates	Start of doWork freeMemory: 8644632; totalMemory: 9109504; maxMemory: 1908932608
    141. 

  141. INFO	2011-05-12 14:34:28	MarkDuplicates	Reading input file and constructing read end information.
    142. 

  142. INFO	2011-05-12 14:34:28	MarkDuplicates	Will retain up to 7575129 data points before spilling to disk.
    143. 

  143. INFO	2011-05-12 14:34:28	MarkDuplicates	Read 7 records. 0 pairs never matched.
    144. 

  144. INFO	2011-05-12 14:34:29	MarkDuplicates	After buildSortedReadEndLists freeMemory: 8316168; totalMemory: 130351104; maxMemory: 1908932608
    145. 

  145. INFO	2011-05-12 14:34:29	MarkDuplicates	Will retain up to 59654144 duplicate indices before spilling to disk.
    146. 

  146. INFO	2011-05-12 14:34:29	MarkDuplicates	Traversing read pair information and detecting duplicates.
    147. 

  147. INFO	2011-05-12 14:34:29	MarkDuplicates	Traversing fragment information and detecting duplicates.
    148. 

  148. INFO	2011-05-12 14:34:29	MarkDuplicates	Sorting list of duplicate records.
    149. 

  149. INFO	2011-05-12 14:34:29	MarkDuplicates	After generateDuplicateIndexes freeMemory: 129615120; totalMemory: 607649792; maxMemory: 1908932608
    150. 

  150. INFO	2011-05-12 14:34:29	MarkDuplicates	Marking 3 records as duplicates.
    151. 

  151. INFO	2011-05-12 14:34:29	MarkDuplicates	Found 0 optical duplicate clusters.
    152. 

  152. INFO	2011-05-12 14:34:29	MarkDuplicates	Before output close freeMemory: 128997520; totalMemory: 607649792; maxMemory: 1908932608
    153. 

  153. INFO	2011-05-12 14:34:29	MarkDuplicates	After output close freeMemory: 128997280; totalMemory: 607649792; maxMemory: 1908932608
    154. 

  154. [Thu May 12 14:34:29 EDT 2011] net.sf.picard.sam.MarkDuplicates done.
    155. 

  155. Runtime.totalMemory()=607649792
    156. 

  156. 

  157. 

  158. </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 
    159. 

  159. generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>
    160. 

  160. 

  161.