Mercurial > repos > jpruab > jpr_picard
diff test-data/picard_output_markdups_sortedpairsam.sam @ 4:f4d018471628 draft default tip
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| author | jpruab |
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| date | Tue, 13 Aug 2013 12:09:14 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_output_markdups_sortedpairsam.sam Tue Aug 13 12:09:14 2013 -0400 @@ -0,0 +1,63 @@ +<?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 rgPicardMarkDups.py tool output - see http://g2.trac.bx.psu.edu/" /> + <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> + </head> + <body> + <div class="document"> + <h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardMarkDups.py run at 19/11/2010 18:25:23</h3> + <b>Your job produced the following outputs - check here for a record of what was done and any unexpected events</b> + <hr /> + <div> + <b>Output files.</b> + <table> + <tr><td><a href="rgPicardMarkDups.txt">rgPicardMarkDups.txt (1.8 KB)</a></td></tr> + </table> + </div> + <hr /> + <div> + <b>Log of activity</b> + <hr/> + ## 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: +<BR /> +[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 +<BR /> +INFO 2010-11-19 18:25:23 MarkDuplicates Start of doWork freeMemory: 8645600; totalMemory: 9109504; maxMemory: 1908932608 +<BR /> +INFO 2010-11-19 18:25:23 MarkDuplicates Reading input file and constructing read end information. +<BR /> +INFO 2010-11-19 18:25:23 MarkDuplicates Will retain up to 7575129 data points before spilling to disk. +<BR /> +[Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates done. +<BR /> +Runtime.totalMemory()=130351104 +<BR /> +Exception in thread "main" net.sf.picard.PicardException: /share/shared/relul.galaxy/database/files/000/dataset_57.dat is not coordinate sorted. +<BR /> + at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:248) +<BR /> + at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109) +<BR /> + at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165) +<BR /> + at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93) +<BR /> + +<BR /> + + </div> + + <div> + <p>Note: The freely available + <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> + generated all outputs reported here. These third party tools were orchestrated by the Galaxy + rgPicardMarkDups.py wrapper and this command line from the Galaxy form: + </p> + <hr /> + <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> + </div> + </body> +</html>