CNVDiscovery error: Unable to create BasicFeatureReader using feature file

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INFO 15:40:32,346 FunctionEdge - Output written to /sge/work/cnv_stage2/seq_chr16/logs/CNVDiscoveryStage2-161.out
INFO 15:40:32,377 DrmaaJobRunner - Submitted job id: 1021427
INFO 15:40:32,377 QGraph - 5 Pend, 1 Run, 0 Fail, 160 Done
ERROR 15:41:02,546 FunctionEdge - Error: 'java' '-Xmx2048m' '-XX:+UseParallelOldGC' '-XX:ParallelGCThreads=4' '-XX:GCTimeLimit=50' '-XX:GCHeapFreeLimit=10' '-Djava.io.tmpdir=/sget/13.ruan_SVt
ERROR 15:41:02,552 FunctionEdge - Contents of /sge/work/cnv_stage2/seq_chr16/logs/CNVDiscoveryStage2-161.out:
INFO 15:40:54,125 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 15:40:54,128 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.5.GS-r1661-0-g49c0dfe, Compiled 2016/05/17 12:41:28
INFO 15:40:54,129 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 15:40:54,129 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 15:40:54,133 HelpFormatter - Program Args: -O /sge/work/cnv_stage2/seq_chr16/seq_chr16.genotypes.annotated.vcf.gz -vcf work/cnv_stage2/seq_chr16/seq_chr16.genotypes.base.
INFO 15:40:54,140 HelpFormatter - Executing as wuzhichao@comput48 on Linux 2.6.32-431.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14.
INFO 15:40:54,140 HelpFormatter - Date/Time: 2016/06/21 15:40:54
INFO 15:40:54,140 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 15:40:54,140 HelpFormatter - -----------------------------------------------------------------------------------------
INFO 15:40:55,050 21-Jun-2016 GenomeAnalysisEngine - Strictness is SILENT
INFO 15:40:55,231 21-Jun-2016 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 15:40:55,250 21-Jun-2016 IntervalUtils - Processing 1 bp from intervals
INFO 15:40:56,119 21-Jun-2016 GenomeAnalysisEngine - Preparing for traversal
INFO 15:40:56,120 21-Jun-2016 GenomeAnalysisEngine - Done preparing for traversal
INFO 15:40:56,120 21-Jun-2016 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 15:40:56,121 21-Jun-2016 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 15:40:56,121 21-Jun-2016 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 15:40:56,148 21-Jun-2016 MetaData - Opening metadata ...
INFO 15:40:56,148 21-Jun-2016 MetaData - Adding metadata directory work/preprocess_output_metadata_directory ...
INFO 15:40:56,151 21-Jun-2016 MetaData - Opened metadata.

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

htsjdk.tribble.TribbleException$MalformedFeatureFile: Unable to create BasicFeatureReader using feature file , for input source: work/cnv_stage2/seq_chr16/seq_chr16.genotypes.base.annotated.vcf.gz
at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:92)
at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:66)
at org.broadinstitute.sv.util.vcf.VCFReader.(VCFReader.java:46)
at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.createVCFHeader(SVVariantAnnotatorWalker.java:319)
at org.broadinstitute.sv.annotation.SVVariantAnnotatorWalker.initialize(SVVariantAnnotatorWalker.java:113)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.sv.main.SVCommandLine.execute(SVCommandLine.java:133)
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.sv.main.SVCommandLine.main(SVCommandLine.java:87)
at org.broadinstitute.sv.main.SVAnnotator.main(SVAnnotator.java:92)
Caused by: java.io.IOException: Unexpected compressed block length: 1
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:377)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:127)
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:252)
at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:188)
at htsjdk.tribble.readers.TabixReader.readIndex(TabixReader.java:242)
at htsjdk.tribble.readers.TabixReader.(TabixReader.java:134)
at htsjdk.tribble.readers.TabixReader.(TabixReader.java:110)
at htsjdk.tribble.TabixFeatureReader.(TabixFeatureReader.java:72)
at htsjdk.tribble.AbstractFeatureReader.getFeatureReader(AbstractFeatureReader.java:85)
... 12 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5.GS-r1661-0-g49c0dfe):
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: Unable to create BasicFeatureReader using feature file , for input source: work/cnv_stage2/seq_chr16/seq_chr16.genotypes.base.annotated.vcf.gz
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