java conflict on cluster
Posted in Ask the team | Last updated on 2013-06-25 17:02:05


Comments (10)

Hi,

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.

Cheers,

Blue

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.

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