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java conflict on cluster
I'm getting repeated errors relating to java, when using GATK in a shell script on my university cluster. The message is 'NoClassDefFoundError'. It has worked previously using GATK version 2.1.9 (on a different node). My memory allocation for GATK on the cluster is set to 16GB. As I'm using GATK as part of a shell script which invokes java, then the 'java', '-2xmg' and '.jar' parts of the command are not required (at least they weren't previously). Attempting to invoke GATK from the command line in cluster using -bash: /cm/shared/apps/GenomeAnalysisTK/2.1.9/GenomeAnalysisTK.jar ...returns :Permission denied
The first question is 'am I coding it correctly?', the second is 'could GATK not be happy with java?' and the third is 'do you have any tips to resolve this?'
I have read the several of the answers relating to java-GATK problems but am none the wiser. Any help would be most appreciated.
The shell script commands are:
#!/bin/sh #$ -N ReadMapper_H001 #$ -S /bin/sh # Reference file IO (.e and .o files) to the current working directory #$ -cwd #Merge the standard out and standard error to one file #$ -j y #Use the bioinf.q #$ -q bioinf.q . /etc/profile.d/modules.sh # Load modules module load bio/1.15 gatk/2.4.9 jdk/1.6.0_24 picard-tools/1.77 R/2.14.0 # All the other stuff (scythe, sickle, bwa, picard etc for cleaning, read mapping etc) # Identify indels from reference genome GenomeAnalysisTK \ -I /mnt/lustre/scratch/bioenv/wg39/tmp/lhm_read_mapping/H001/H001_CRSN.bam \ -R /home/w/wg/wg39/accessory_data_130613/Dmel_ref_seqs_051112/dmel-all-chromosome-r5.9.fasta \ -T RealignerTargetCreator \ -o /mnt/lustre/scratch/bioenv/wg39/tmp/lhm_read_mapping/H001/H001_realignment.intervals \ --filter_mismatching_base_and_quals The error message is: untime.totalMemory()=1750597632 Exception in thread "main" java.lang.NoClassDefFoundError: java Caused by: java.lang.ClassNotFoundException: java 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) Could not find the main class: java. Program will exit.