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Old 02-11-2013, 11:01 AM   #1
chongm
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Location: Canada

Join Date: Sep 2012
Posts: 21
Default Picard Collect Insert Size Java Problem

Hi Everyone:

I was trying to generate histograms for insert size using Picard's "CollectInsertSizeMetrics" but came across an error.


I ran the following code:

java -Xmx4g -Djava.io.tmpdir=${data}/${i}/tmp \
-jar $CollectInsertSizeMetrics \
INPUT=${i}.duplicates.bam \
OUTPUT=${i}.duplicates.insertsize.metrics \
METRIC_ACCUMULATION_LEVEL=ALL_READS \
HISTOGRAM_WIDTH=10 \
HISTOGRAM_FILE=${i}.duplicates.insertsize.histogram
done

Which gave me this error message:

####### ERROR IN MAKING THE HISTOGRAMS
FAQ: http://sourceforge.net/apps/mediawik...itle=Main_Page
Exception in thread "main" net.sf.picard.PicardException: Unexpected exception creating R script file
at net.sf.picard.util.RExecutor.writeScriptFile(RExecutor.java:92)
at net.sf.picard.util.RExecutor.executeFromClasspath(RExecutor.java:54)
at net.sf.picard.analysis.CollectInsertSizeMetrics.finish(CollectInsertSizeMetrics.java:139)
at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:138)
at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:55)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
at net.sf.picard.analysis.CollectInsertSizeMetrics.main(CollectInsertSizeMetrics.java:82)
Caused by: java.io.IOException: No such file or directory
at java.io.UnixFileSystem.createFileExclusively(Native Method)
at java.io.File.checkAndCreate(Unknown Source)
at java.io.File.createTempFile(Unknown Source)
at java.io.File.createTempFile(Unknown Source)
at net.sf.picard.util.RExecutor.writeScriptFile(RExecutor.java:87)
... 7 more

Any help would be appreciated
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