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ERROR DURING FILTERING VARIANT STEP

satish86satish86 AshevilleMember

Hi ,

I am trying to filter my variants only if they have covergare of >=10, Below is the error I am getting

$ java -jar /opt/NGSTools/GATK-3.2.2/GenomeAnalysisTK.jar -T VariantFiltration -R /home/data/GATK_test/gatk/ucsc.hg19.fasta --variant 12-0116KZ_vcf_snp-indel.vcf -o 12-
0116KZ__filtered.vcf --filterExpression "DP > 10"
INFO 12:59:02,106 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:59:02,108 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03
INFO 12:59:02,109 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 12:59:02,109 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 12:59:02,113 HelpFormatter - Program Args: -T VariantFiltration -R /home/data/GATK_test/gatk/ucsc.hg19.fasta --variant 12-0116KZ_vcf_snp-indel.vcf -o 12-0116KZ__filtered.vcf --filterExpression DP > 10
INFO 12:59:02,123 HelpFormatter - Executing as [email protected] on Linux 2.6.32-431.23.3.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_65-mockbuild_2014_07_14_06_19-b00.
INFO 12:59:02,124 HelpFormatter - Date/Time: 2014/10/22 12:59:02
INFO 12:59:02,124 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:59:02,124 HelpFormatter - --------------------------------------------------------------------------------
INFO 12:59:02,199 GenomeAnalysisEngine - Strictness is SILENT
INFO 12:59:02,352 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 12:59:02,487 GenomeAnalysisEngine - Preparing for traversal
INFO 12:59:02,508 GenomeAnalysisEngine - Done preparing for traversal
INFO 12:59:02,508 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 12:59:02,509 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 12:59:02,509 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
WARN 12:59:03,266 RestStorageService - Error Response: PUT '/yzrGUOlIfLoDxQzDGnPauLbDm4fD0TwM.report.xml.gz' -- ResponseCode: 403, ResponseStatus: Forbidden, Request Headers: [Content-Length: 809, Content-MD5: BxyNhjXmVTFtPLFC1PfHvQ==, Content-Type: application/octet-stream, x-amz-meta-md5-hash: 071c8d8635e655316d3cb142d4f7c7bd, Date: Wed, 22 Oct 2014 17:59:02 GMT, Authorization: AWS AKIAI22FBBJ37D5X62OQ:xPIn4b04nmKanO/VjUHgupuql8w=, User-Agent: JetS3t/0.8.1 (Linux/2.6.32-431.23.3.el6.x86_64; amd64; en; JVM 1.7.0_65), Host: broad.gsa.gatk.run.reports.s3.amazonaws.com, Expect: 100-continue], Response Headers: [x-amz-request-id: 7CC503EC75535B0F, x-amz-id-2: fAfDXCnwIDLYgjwyQf84lgZBbHe/DyKdCzO2K5I3pQXQPC8kSeRu/ceSKfd2FS3I, Content-Type: application/xml, Transfer-Encoding: chunked, Date: Wed, 22 Oct 2014 21:58:59 GMT, Connection: close, Server: AmazonS3]
WARN 12:59:03,415 RestStorageService - Adjusted time offset in response to RequestTimeTooSkewed error. Local machine and S3 server disagree on the time by approximately 14396 seconds. Retrying connection.
INFO 12:59:03,557 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.IllegalArgumentException: Inconsistent number of provided filter names and expressions: names=[] exps=[DP > 10]
at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:238)
at htsjdk.variant.variantcontext.VariantContextUtils.initializeMatchExps(VariantContextUtils.java:249)
at org.broadinstitute.gatk.tools.walkers.filters.VariantFiltration.initialize(VariantFiltration.java:230)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Inconsistent number of provided filter names and expressions: names=[] exps=[DP > 10]
ERROR ------------------------------------------------------------------------------------------

Any help will be appreciated.

Satish

Answers

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