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- + 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.
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