An error happened in CombineGVCFs :Unable to create iterator for rod named variant4

Hello everyone,
I met an error when I do combineGVCFs with the command line as follow:
java -Xmx500g -Djava.io.tmpdir=goat_pan/tmp -jar GenomeAnalysisTK.jar -R ASM.fa \
-T CombineGVCFs \
--variant Wm102-3.genotype.g.vcf.gz \
--variant Wme01-3.genotype.g.vcf.gz \
--variant Wme02-3.genotype.g.vcf.gz \
--variant xme02-6.genotype.g.vcf.gz \
--variant Xmr01-1.genotype.g.vcf.gz \
--variant Xmr01-6.genotype.g.vcf.gz \
--variant xmr02-6.genotype.g.vcf.gz \
-o goat.merge.g.vcf.gz
And the error lines are as follow:

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

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to create iterator for rod named variant4
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:248)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:185)
at org.broadinstitute.gatk.engine.datasources.rmd.ResourcePool.iterator(ResourcePool.java:93)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:168)
at org.broadinstitute.gatk.engine.datasources.providers.RodLocusView.(RodLocusView.java:82)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.getLocusView(TraverseLociNano.java:129)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:80)
at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
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:106)
Caused by: htsjdk.samtools.SAMFormatException: Invalid GZIP header
at htsjdk.samtools.util.BlockGunzipper.unzipBlock(BlockGunzipper.java:72)
at htsjdk.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:402)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:384)
at htsjdk.samtools.util.BlockCompressedInputStream.seek(BlockCompressedInputStream.java:292)
at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:382)
at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:45)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:162)
at htsjdk.tribble.TabixFeatureReader$FeatureIterator.(TabixFeatureReader.java:150)
at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:125)
at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrack.query(RMDTrack.java:119)
at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:241)
... 13 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5-0-g36282e4):
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 iterator for rod named variant4
ERROR ------------------------------------------------------------------------------------------

Thank you !!!

Answers

  • valentinvalentin Cambridge, MAMember, Dev

    Looking at the message of the causing exception "Invalid GZIP header"
    It seems to indicate that one of the input files gzip is somehow "corrupt"? My first guess is that 'variant4' makes reference to the forth --variant file in your command line "xme02-6.genotype.g.vcf.gz" but it could be any (perhaps is not based on command line order or the first variant is named variant0)'. Besides are those .gz files generated with gzip or bgzip? it might be the case that GATK expect it to be the latter.

  • Hi,valentin,
    Thank you for your reply.
    The first variant name is variant,so the variant4 is xme02-6.genotype.g.vcf.gz.
    I checked the xme02-6.sort.dedup.bam and I am sure that it is ok .
    I don't know what 's the problem so I rerun the gvcf of this sample with my CMD in a shell:
    file="Wmr01-3
    "
    for i in $file
    do
    java -Xmx100g -jar ~/software/GenomeAnalysisTK.jar -R goat_pan/my_clean_data/bwa_mem/ASM.fa \
    -T HaplotypeCaller \
    -I $i'.sort.dedup.bam' \
    -o $i'.genotype.g.vcf.gz' \
    -stand_emit_conf 30 \
    -stand_call_conf 10 \
    --genotyping_mode DISCOVERY \
    -ERC GVCF

    done

    Now it is running so I will come back to report the result later.

    Thank you again.

    yours
    xiangyu pan

  • @valentin said:
    Looking at the message of the causing exception "Invalid GZIP header"
    It seems to indicate that one of the input files gzip is somehow "corrupt"? My first guess is that 'variant4' makes reference to the forth --variant file in your command line "xme02-6.genotype.g.vcf.gz" but it could be any (perhaps is not based on command line order or the first variant is named variant0)'. Besides are those .gz files generated with gzip or bgzip? it might be the case that GATK expect it to be the latter.

    Thank you for your reply.I 've sovle this question.I rerun the variant4 file and then merge is sucessful.
    So it must be a truncated file.
    Thank you again!

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