java cp issue

+ sh -x run.sh
+ export '_JAVA_OPTIONS=-Xms1g -Xmx10g'
+ _JAVA_OPTIONS='-Xms1g -Xmx10g'
+ java -cp /apps/gatk/3.2.2/jexl.jar -jar /apps/gatk/3.2.2/GenomeAnalysisTK.jar -T VariantFiltration -R /bio/kirst/Poplar_association/Indexed_updated_ref/Ptrichocarpa_156_updated_with_deltoides_inferred_032013.fasta -V raw_snps_full_population.vcf --filterExpression 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0' --filterName gatk_recom -o filtered_snps_full_population.vcf
Picked up _JAVA_OPTIONS: -Xms1g -Xmx10g
INFO  18:01:35,082 HelpFormatter - --------------------------------------------------------------------------------
INFO  18:01:35,085 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03
INFO  18:01:35,085 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  18:01:35,085 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  18:01:35,092 HelpFormatter - Program Args: -T VariantFiltration -R /bio/kirst/Poplar_association/Indexed_updated_ref/Ptrichocarpa_156_updated_with_deltoides_inferred_032013.fasta -V raw_snps_full_population.vcf --filterExpression QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0 --filterName gatk_recom -o filtered_snps_full_population.vcf
INFO  18:01:35,096 HelpFormatter - Executing as afahrenk@c10a-s8.ufhpc on Linux 2.6.32-358.23.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_02-b13.
INFO  18:01:35,097 HelpFormatter - Date/Time: 2014/09/18 18:01:35
INFO  18:01:35,097 HelpFormatter - --------------------------------------------------------------------------------
INFO  18:01:35,097 HelpFormatter - --------------------------------------------------------------------------------
INFO  18:01:36,665 GenomeAnalysisEngine - Strictness is SILENT

+ sh -x run_gatk.sh
+ export '_JAVA_OPTIONS=-Xms1g -Xmx10g'
+ _JAVA_OPTIONS='-Xms1g -Xmx10g'
+ sh -x GATK -T VariantFiltration -R /bio/kirst/Poplar_association/Indexed_updated_ref/Ptrichocarpa_156_updated_with_deltoides_inferred_032013.fasta -V raw_snps_full_population.vcf --filterExpression 'QD < 2.0 || FS > 60.0 || MQ < 40.0 || HaplotypeScore > 13.0 || MappingQualityRankSum < -12.5 || ReadPosRankSum < -8.0' --filterName gatk_recom -o filtered_snps_full_population.vcf
+ [[ -z -Xms1g -Xmx10g ]]
+ echo 'Calling GenomeAnalysisTk from GATK wrapper'
Calling GenomeAnalysisTk from GATK wrapper
+ which java
/usr/java/jdk1.7.0_02/bin/java
+ java -cp /apps/gatk/3.2.2/jexl.jar -jar /apps/gatk/3.2.2/GenomeAnalysisTK.jar -T VariantFiltration -R /bio/kirst/Poplar_association/Indexed_updated_ref/Ptrichocarpa_156_updated_with_deltoides_inferred_032013.fasta -V raw_snps_full_population.vcf --filterExpression QD '<' 2.0 '||' FS '>' 60.0 '||' MQ '<' 40.0 '||' HaplotypeScore '>' 13.0 '||' MappingQualityRankSum '<' -12.5 '||' ReadPosRankSum '<' -8.0 --filterName gatk_recom -o filtered_snps_full_population.vcf
Picked up _JAVA_OPTIONS: -Xms1g -Xmx10g
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.2-2-gec30cee):
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.