/test-data/picard_output_insertsize_tinysam.html
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1<style type="text/css"> 2 tr.d0 td {background-color: oldlace; color: black;} 3 tr.d1 td {background-color: aliceblue; color: black;} 4 </style><?xml version="1.0" encoding="utf-8" ?> 5<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> 6<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 7<head> 8<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> 9<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> 10<title></title> 11<link rel="stylesheet" href="/static/style/base.css" type="text/css" /> 12</head> 13<body> 14<div class="document"> 15Galaxy 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 39WARNING 2011-05-13 15:20:45 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. 40INFO 2011-05-13 15:20:46 ProcessExecutor [1] "FR = red" "RF = blue" 41INFO 2011-05-13 15:20:46 ProcessExecutor null device 42INFO 2011-05-13 15:20:46 ProcessExecutor 1 43[Fri May 13 15:20:46 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics done. 44Runtime.totalMemory()=9109504 45 46 47INFO: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 48 49INFO: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 50 51</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> 52generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> 53