Mercurial > repos > devteam > picard
view test-data/picard_output_markdups_sortedpairsam.html @ 2:9227b8c3093b
Updated command line format per dev team standards.
| author | devteam <devteam@galaxyproject.org> |
|---|---|
| date | Tue, 02 Apr 2013 09:42:36 -0400 |
| parents | 1cd7f3b42609 |
| children |
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<style type="text/css"> tr.d0 td {background-color: oldlace; color: black;} tr.d1 td {background-color: aliceblue; color: black;} </style><?xml version="1.0" encoding="utf-8" ?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> <title></title> <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> </head> <body> <div class="document"> 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> <tr><td><a href="MarkDuplicates.log">MarkDuplicates.log</a></td></tr> <tr><td><a href="MarkDuplicates.metrics.txt">MarkDuplicates.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.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> </td></tr> <tr class="d1"><td>UNPAIRED_READS_EXAMINED</td><td>1 </td></tr> <tr class="d0"><td>READ_PAIRS_EXAMINED</td><td>3 </td></tr> <tr class="d1"><td>UNMAPPED_READS</td><td>1 </td></tr> <tr class="d0"><td>UNPAIRED_READ_DUPLICATES</td><td>1 </td></tr> <tr class="d1"><td>READ_PAIR_DUPLICATES</td><td>1 </td></tr> <tr class="d0"><td>READ_PAIR_OPTICAL_DUPLICATES</td><td>0 </td></tr> <tr class="d1"><td>PERCENT_DUPLICATION</td><td>0.428571 </td></tr> <tr class="d0"><td>ESTIMATED_LIBRARY_SIZE </td><td>3 </td></tr> <tr class="d0"><td colspan="2">## HISTOGRAM java.lang.Double</td></tr><tr class="d0"><td colspan="2">BIN VALUE</td></tr> <tr class="d1"><td colspan="2">1.0 0.948181</td></tr> <tr class="d0"><td colspan="2">2.0 1.296997</td></tr> <tr class="d1"><td colspan="2">3.0 1.425319</td></tr> <tr class="d0"><td colspan="2">4.0 1.472527</td></tr> <tr class="d1"><td colspan="2">5.0 1.489893</td></tr> <tr class="d0"><td colspan="2">6.0 1.496282</td></tr> <tr class="d1"><td colspan="2">7.0 1.498632</td></tr> <tr class="d0"><td colspan="2">8.0 1.499497</td></tr> <tr class="d1"><td colspan="2">9.0 1.499815</td></tr> <tr class="d0"><td colspan="2">10.0 1.499932</td></tr> <tr class="d1"><td colspan="2">11.0 1.499975</td></tr> <tr class="d0"><td colspan="2">12.0 1.499991</td></tr> <tr class="d1"><td colspan="2">13.0 1.499997</td></tr> <tr class="d0"><td colspan="2">14.0 1.499999</td></tr> <tr class="d1"><td colspan="2">15.0 1.5</td></tr> <tr class="d0"><td colspan="2">16.0 1.5</td></tr> <tr class="d1"><td colspan="2">17.0 1.5</td></tr> <tr class="d0"><td colspan="2">18.0 1.5</td></tr> <tr class="d1"><td colspan="2">19.0 1.5</td></tr> <tr class="d0"><td colspan="2">20.0 1.5</td></tr> <tr class="d1"><td colspan="2">21.0 1.5</td></tr> <tr class="d0"><td colspan="2">22.0 1.5</td></tr> <tr class="d1"><td colspan="2">23.0 1.5</td></tr> <tr class="d0"><td colspan="2">24.0 1.5</td></tr> <tr class="d1"><td colspan="2">25.0 1.5</td></tr> <tr class="d0"><td colspan="2">26.0 1.5</td></tr> <tr class="d1"><td colspan="2">27.0 1.5</td></tr> <tr class="d0"><td colspan="2">28.0 1.5</td></tr> <tr class="d1"><td colspan="2">29.0 1.5</td></tr> <tr class="d0"><td colspan="2">30.0 1.5</td></tr> <tr class="d1"><td colspan="2">31.0 1.5</td></tr> <tr class="d0"><td colspan="2">32.0 1.5</td></tr> <tr class="d1"><td colspan="2">33.0 1.5</td></tr> <tr class="d0"><td colspan="2">34.0 1.5</td></tr> <tr class="d1"><td colspan="2">35.0 1.5</td></tr> <tr class="d0"><td colspan="2">36.0 1.5</td></tr> <tr class="d1"><td colspan="2">37.0 1.5</td></tr> <tr class="d0"><td colspan="2">38.0 1.5</td></tr> <tr class="d1"><td colspan="2">39.0 1.5</td></tr> <tr class="d0"><td colspan="2">40.0 1.5</td></tr> <tr class="d1"><td colspan="2">41.0 1.5</td></tr> <tr class="d0"><td colspan="2">42.0 1.5</td></tr> <tr class="d1"><td colspan="2">43.0 1.5</td></tr> <tr class="d0"><td colspan="2">44.0 1.5</td></tr> <tr class="d1"><td colspan="2">45.0 1.5</td></tr> <tr class="d0"><td colspan="2">46.0 1.5</td></tr> <tr class="d1"><td colspan="2">47.0 1.5</td></tr> <tr class="d0"><td colspan="2">48.0 1.5</td></tr> <tr class="d1"><td colspan="2">49.0 1.5</td></tr> <tr class="d0"><td colspan="2">50.0 1.5</td></tr> <tr class="d1"><td colspan="2">51.0 1.5</td></tr> <tr class="d0"><td colspan="2">52.0 1.5</td></tr> <tr class="d1"><td colspan="2">53.0 1.5</td></tr> <tr class="d0"><td colspan="2">54.0 1.5</td></tr> <tr class="d1"><td colspan="2">55.0 1.5</td></tr> <tr class="d0"><td colspan="2">56.0 1.5</td></tr> <tr class="d1"><td colspan="2">57.0 1.5</td></tr> <tr class="d0"><td colspan="2">58.0 1.5</td></tr> <tr class="d1"><td colspan="2">59.0 1.5</td></tr> <tr class="d0"><td colspan="2">60.0 1.5</td></tr> <tr class="d1"><td colspan="2">61.0 1.5</td></tr> <tr class="d0"><td colspan="2">62.0 1.5</td></tr> <tr class="d1"><td colspan="2">63.0 1.5</td></tr> <tr class="d0"><td colspan="2">64.0 1.5</td></tr> <tr class="d1"><td colspan="2">65.0 1.5</td></tr> <tr class="d0"><td colspan="2">66.0 1.5</td></tr> <tr class="d1"><td colspan="2">67.0 1.5</td></tr> <tr class="d0"><td colspan="2">68.0 1.5</td></tr> <tr class="d1"><td colspan="2">69.0 1.5</td></tr> <tr class="d0"><td colspan="2">70.0 1.5</td></tr> <tr class="d1"><td colspan="2">71.0 1.5</td></tr> <tr class="d0"><td colspan="2">72.0 1.5</td></tr> <tr class="d1"><td colspan="2">73.0 1.5</td></tr> <tr class="d0"><td colspan="2">74.0 1.5</td></tr> <tr class="d1"><td colspan="2">75.0 1.5</td></tr> <tr class="d0"><td colspan="2">76.0 1.5</td></tr> <tr class="d1"><td colspan="2">77.0 1.5</td></tr> <tr class="d0"><td colspan="2">78.0 1.5</td></tr> <tr class="d1"><td colspan="2">79.0 1.5</td></tr> <tr class="d0"><td colspan="2">80.0 1.5</td></tr> <tr class="d1"><td colspan="2">81.0 1.5</td></tr> <tr class="d0"><td colspan="2">82.0 1.5</td></tr> <tr class="d1"><td colspan="2">83.0 1.5</td></tr> <tr class="d0"><td colspan="2">84.0 1.5</td></tr> <tr class="d1"><td colspan="2">85.0 1.5</td></tr> <tr class="d0"><td colspan="2">86.0 1.5</td></tr> <tr class="d1"><td colspan="2">87.0 1.5</td></tr> <tr class="d0"><td colspan="2">88.0 1.5</td></tr> <tr class="d1"><td colspan="2">89.0 1.5</td></tr> <tr class="d0"><td colspan="2">90.0 1.5</td></tr> <tr class="d1"><td colspan="2">91.0 1.5</td></tr> <tr class="d0"><td colspan="2">92.0 1.5</td></tr> <tr class="d1"><td colspan="2">93.0 1.5</td></tr> <tr class="d0"><td colspan="2">94.0 1.5</td></tr> <tr class="d1"><td colspan="2">95.0 1.5</td></tr> <tr class="d0"><td colspan="2">96.0 1.5</td></tr> <tr class="d1"><td colspan="2">97.0 1.5</td></tr> <tr class="d0"><td colspan="2">98.0 1.5</td></tr> <tr class="d1"><td colspan="2">99.0 1.5</td></tr> </table> <b>Picard Tool Run Log</b><hr/> <pre>Thu, 12 May 2011 14:34:29 INFO ## 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: [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 INFO 2011-05-12 14:34:28 MarkDuplicates Start of doWork freeMemory: 8644632; totalMemory: 9109504; maxMemory: 1908932608 INFO 2011-05-12 14:34:28 MarkDuplicates Reading input file and constructing read end information. INFO 2011-05-12 14:34:28 MarkDuplicates Will retain up to 7575129 data points before spilling to disk. INFO 2011-05-12 14:34:28 MarkDuplicates Read 7 records. 0 pairs never matched. INFO 2011-05-12 14:34:29 MarkDuplicates After buildSortedReadEndLists freeMemory: 8316168; totalMemory: 130351104; maxMemory: 1908932608 INFO 2011-05-12 14:34:29 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk. INFO 2011-05-12 14:34:29 MarkDuplicates Traversing read pair information and detecting duplicates. INFO 2011-05-12 14:34:29 MarkDuplicates Traversing fragment information and detecting duplicates. INFO 2011-05-12 14:34:29 MarkDuplicates Sorting list of duplicate records. INFO 2011-05-12 14:34:29 MarkDuplicates After generateDuplicateIndexes freeMemory: 129615120; totalMemory: 607649792; maxMemory: 1908932608 INFO 2011-05-12 14:34:29 MarkDuplicates Marking 3 records as duplicates. INFO 2011-05-12 14:34:29 MarkDuplicates Found 0 optical duplicate clusters. INFO 2011-05-12 14:34:29 MarkDuplicates Before output close freeMemory: 128997520; totalMemory: 607649792; maxMemory: 1908932608 INFO 2011-05-12 14:34:29 MarkDuplicates After output close freeMemory: 128997280; totalMemory: 607649792; maxMemory: 1908932608 [Thu May 12 14:34:29 EDT 2011] net.sf.picard.sam.MarkDuplicates done. Runtime.totalMemory()=607649792 </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>