Question: error while using picard 2.1.0
1
gravatar for kirannbishwa01
3.9 years ago by
kirannbishwa011.2k
United States
kirannbishwa011.2k wrote:

I have been using picard for a while and it was working good. I just downloaded a new version of picard 2.1.0. While the previous upgrades worked fine the recent picard does not seem to respond and is giving me error message related to java.

Since the jar files are executable using java I put both version in different folders and tried to run them with the same samples and same commands:

Picard version 1.139:

java -jar /home/everestial007/picard-tools-1.139/picard.jar CleanSam I=SAMPEaligned_MA605readsBWA.sam O=clean_ aligned_MA605readsBWA.sam

works perfectly

 

Picard version 2.1.0:

java -jar /home/everestial007/picard-tools-2.1.0/picard.jar CleanSam I=SAMPEaligned_MA605readsBWA.sam O=clean_ aligned_Pi2_MA605readsBWA.sam

gives me error message -

Exception in thread "main" java.lang.UnsupportedClassVersionError: picard/cmdline/PicardCommandLine : Unsupported major.minor version 52.0
    at java.lang.ClassLoader.defineClass1(Native Method)
    at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
    at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
    at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
    at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
    at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
    at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
    at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)

 

I never had this issue before and my hunch is that it may or may not be related with java. But, I am little hesitant to update my java as it may turn out not working for other apps that I am currently running.

Any suggestions is appreciated.

 

cleansam alignment picard gatk • 2.0k views
ADD COMMENTlink modified 3.9 years ago by RamRS25k • written 3.9 years ago by kirannbishwa011.2k
4
gravatar for genomax
3.9 years ago by
genomax76k
United States
genomax76k wrote:

As of version 2.0.1 (Nov. 2015) Picard requires Java 1.8 (jdk8u66).

ADD COMMENTlink written 3.9 years ago by genomax76k

Thanks it helped !

ADD REPLYlink written 3.9 years ago by kirannbishwa011.2k
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