command-line tool error xtools/gsea/Gsea : Unsupported major.minor version 52.0
ceb...@case.edu
I am running into heap space issues trying to use the GO-biological processes gene set list on the desktop application. To try and get around the memory problem, I copied the command line from the desktop application and tried to run it on my terminal. I downloaded the gsea-3.0.jar file from the downloads page, but I cannot get the command to execute. I have tried stripping down the command to see where it breaks. It appears that it can run the .jar script, but gets hung up on the xtool. See below for details. I am running Java 8 (I also tried Java 10 and attempted to find Java 9, but this didn't help) Everything was downloaded and installed within the last week. I have also tried the GSEA Desktop 1gig, 4gig and 8gig.
java -cp /Volumes/padgetrlab/RNA-Seq_IndexedReads_2017/Matt_GSEA_Analysis/gsea-3.0.jar -Xmx512m xtools.gsea.Gsea -res /Volumes/padgetrlab/RNA-Seq_IndexedReads_2017/Matt_GSEA_Analysis/Input_files/DDX41_R525H_v_OE.txt -cls /Users/hershbc/gsea_home/output/may10/DDX41_R525H_vs_DDX41_OE.cls#DDX41_R525H_versus_DDX41_OE -gmx gseaftp.broadinstitute.org://pub/gsea/gene_sets_final/c5.all.v6.1.symbols.gmt -collapse false -mode Max_probe -norm meandiv -nperm 1000 -permute gene_set -rnd_type no_balance -scoring_scheme weighted -rpt_label my_analysis -metric Signal2Noise -sort real -order descending -create_gcts false -create_svgs false -include_only_symbols true -make_sets true -median false -num 100 -plot_top_x 20 -rnd_seed timestamp -save_rnd_lists false -set_max 500 -set_min 15 -zip_report false -out /Users/hershbc/gsea_home/output/may10 -gui false
Exception in thread "main" java.lang.UnsupportedClassVersionError: xtools/gsea/Gsea : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
Try to execute script:
java -cp /Volumes/padgetrlab/RNA-Seq_IndexedReads_2017/Matt_GSEA_Analysis/gsea-3.0.jar -Xmx512m
Usage: java [-options] class [args...]
(to execute a class)
or java [-options] -jar jarfile [args...]
(to execute a jar file)
*seems to work
Try to execute script with tool name: Gsea
lri-106941:~ hershbc$ java -cp /Volumes/padgetrlab/RNA-Seq_IndexedReads_2017/Matt_GSEA_Analysis/gsea-3.0.jar -Xmx512m xtools.gsea.Gsea
Exception in thread "main" java.lang.UnsupportedClassVersionError: xtools/gsea/Gsea : Unsupported major.minor version 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClassCond(ClassLoader.java:637)
at java.lang.ClassLoader.defineClass(ClassLoader.java:621)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
David Eby
Just to be clear, at this time GSEA is *only* supported on Oracle Java 8. Unlike most previous releases, Java 9 and 10 are not drop-in backward compatible and require considerable code changes. There have also been bug reports related to OpenJDK so we recommend sticking to the Oracle releases. We haven't had the resources to address these matters but hope to pick up development later in the year.
Regards,
David Eby Consultant Cancer Informatics Development Broad Institute of MIT and Harvard 415 Main St, Cambridge, MA 02142, USA http://www.broadinstitute.org/cancer http://www.gsea-msigdb.org https://twitter.com/GSEA_MSigDB https://twitter.com/GenePattern