Hi all,
I have the following problem when I run the Picard tool CollectInsertSizeMetrics.jar on a SAM file:
>java -jar
INPUT=alignedsorted.bam
OUTPUT=collectgcbiasmetricsoutfile
HISTOGRAMFILE=chartoutputoutfile.pdf VALIDATION_STRINGENCY=LENIENT
This command successfully creates an outfile with the insert size metric raw numbers, but fails to create the histogram file and gives the following error:
---------------------------------------------------------------------------------
Exception in thread "main" net.sf.picard.PicardException: Unexpected exception executing [Rscript /var/folders/LQ/LQtAvdk7FwmOLyjOs72FKU+++TI/-Tmp-/Andy/script7235887036363822816.R /Users/Andy/ngs/pipetest/refgen/collectgcbiasmetricsoutfile /Users/Andy/ngs/pipetest/refgen/chartoutputoutfile.pdf alignedsorted.bam]
at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:102)
at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:78)
at net.sf.picard.util.RExecutor.executeFromFile(RExecutor.java:73)
at net.sf.picard.util.RExecutor.executeFromClasspath(RExecutor.java:55)
at net.sf.picard.analysis.CollectInsertSizeMetrics.finish(CollectInsertSizeMetrics.java:207)
at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:145)
at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117)
at net.sf.picard.analysis.CollectInsertSizeMetrics.main(CollectInsertSizeMetrics.java:81)
Caused by: java.io.IOException: Cannot run program "Rscript": error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at java.lang.Runtime.exec(Runtime.java:466)
at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:93)
... 9 more
Caused by: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.forkAndExec(Native Method)
at java.lang.UNIXProcess.<init>(UNIXProcess.java:53)
at java.lang.ProcessImpl.start(ProcessImpl.java:91)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 12 more
system cd ~/ngs/pipetest/refgen/; java -jar /users/andy/ngs/applications/picard-tools-1.38/CollectInsertSizeMetrics.jar INPUT=alignedsorted.bam OUTPUT=collectgcbiasmetricsoutfile HISTOGRAM_FILE=chartoutputoutfile.pdf VALIDATION_STRINGENCY=LENIENT
---------------------------------------------------------------------------------
If I run the command as above but with
>java jvm-args -jar
The program crashes right away with error message:
---------------------------------------------------------------------------------
Exception in thread "main" java.lang.NoClassDefFoundError: jvm-args
Caused by: java.lang.ClassNotFoundException: jvm-args
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
system cd ~/ngs/pipetest/refgen/; java jvm-args -jar /users/andy/ngs/applications/picard-tools-1.38/CollectInsertSizeMetrics.jar INPUT=alignedsorted.bam OUTPUT=collectgcbiasmetricsoutfile HISTOGRAM_FILE=chartoutputoutfile.pdf VALIDATION_STRINGENCY=LENIENT
---------------------------------------------------------------------------------
I'm a newbie currently learning unix/perl and use of NGS tools. Any ideas what my problem could be?
Any help would be greatly appreciated.
Andy
I have the following problem when I run the Picard tool CollectInsertSizeMetrics.jar on a SAM file:
>java -jar
INPUT=alignedsorted.bam
OUTPUT=collectgcbiasmetricsoutfile
HISTOGRAMFILE=chartoutputoutfile.pdf VALIDATION_STRINGENCY=LENIENT
This command successfully creates an outfile with the insert size metric raw numbers, but fails to create the histogram file and gives the following error:
---------------------------------------------------------------------------------
Exception in thread "main" net.sf.picard.PicardException: Unexpected exception executing [Rscript /var/folders/LQ/LQtAvdk7FwmOLyjOs72FKU+++TI/-Tmp-/Andy/script7235887036363822816.R /Users/Andy/ngs/pipetest/refgen/collectgcbiasmetricsoutfile /Users/Andy/ngs/pipetest/refgen/chartoutputoutfile.pdf alignedsorted.bam]
at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:102)
at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:78)
at net.sf.picard.util.RExecutor.executeFromFile(RExecutor.java:73)
at net.sf.picard.util.RExecutor.executeFromClasspath(RExecutor.java:55)
at net.sf.picard.analysis.CollectInsertSizeMetrics.finish(CollectInsertSizeMetrics.java:207)
at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:145)
at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:156)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117)
at net.sf.picard.analysis.CollectInsertSizeMetrics.main(CollectInsertSizeMetrics.java:81)
Caused by: java.io.IOException: Cannot run program "Rscript": error=2, No such file or directory
at java.lang.ProcessBuilder.start(ProcessBuilder.java:460)
at java.lang.Runtime.exec(Runtime.java:593)
at java.lang.Runtime.exec(Runtime.java:466)
at net.sf.picard.util.ProcessExecutor.execute(ProcessExecutor.java:93)
... 9 more
Caused by: java.io.IOException: error=2, No such file or directory
at java.lang.UNIXProcess.forkAndExec(Native Method)
at java.lang.UNIXProcess.<init>(UNIXProcess.java:53)
at java.lang.ProcessImpl.start(ProcessImpl.java:91)
at java.lang.ProcessBuilder.start(ProcessBuilder.java:453)
... 12 more
system cd ~/ngs/pipetest/refgen/; java -jar /users/andy/ngs/applications/picard-tools-1.38/CollectInsertSizeMetrics.jar INPUT=alignedsorted.bam OUTPUT=collectgcbiasmetricsoutfile HISTOGRAM_FILE=chartoutputoutfile.pdf VALIDATION_STRINGENCY=LENIENT
---------------------------------------------------------------------------------
If I run the command as above but with
>java jvm-args -jar
The program crashes right away with error message:
---------------------------------------------------------------------------------
Exception in thread "main" java.lang.NoClassDefFoundError: jvm-args
Caused by: java.lang.ClassNotFoundException: jvm-args
at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
system cd ~/ngs/pipetest/refgen/; java jvm-args -jar /users/andy/ngs/applications/picard-tools-1.38/CollectInsertSizeMetrics.jar INPUT=alignedsorted.bam OUTPUT=collectgcbiasmetricsoutfile HISTOGRAM_FILE=chartoutputoutfile.pdf VALIDATION_STRINGENCY=LENIENT
---------------------------------------------------------------------------------
I'm a newbie currently learning unix/perl and use of NGS tools. Any ideas what my problem could be?
Any help would be greatly appreciated.
Andy
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