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##### ERROR stack trace ReviewedGATKException: Unable to create iterator for rod named variant

RfahyRfahy Member
edited July 2018 in Ask the GATK team

Full Error Message:

INFO  13:56:19,951 HelpFormatter - ---------------------------------------------------------------------------------- 
INFO  13:56:19,954 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18 
INFO  13:56:19,954 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  13:56:19,954 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk 
INFO  13:56:19,954 HelpFormatter - [Tue Jul 10 13:56:19 MDT 2018] Executing on Linux 3.10.0-693.11.6.el7.x86_64 amd64 
INFO  13:56:19,954 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13 
INFO  13:56:19,957 HelpFormatter - Program Args: --analysis_type FastaAlternateReferenceMaker --reference_sequence /Users/ryfa5051/NGS/bwa_sam_trial/OM_AN_FRAG_REF_FIN.fa --out /Users/ryfa5051/NGS/bwa_sam_trial/fasta/fin/an85266_final.fasta --variant /Users/ryfa5051/NGS/bwa_sam_trial/fasta/picard_renamed_an85266.vcf.gz -IUPAC an85266 
INFO  13:56:19,961 HelpFormatter - Executing as [email protected] on Linux 3.10.0-693.11.6.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13. 
INFO  13:56:19,962 HelpFormatter - Date/Time: 2018/07/10 13:56:19 
INFO  13:56:19,962 HelpFormatter - ---------------------------------------------------------------------------------- 
INFO  13:56:19,962 HelpFormatter - ---------------------------------------------------------------------------------- 
INFO  13:56:19,978 GenomeAnalysisEngine - Strictness is SILENT 
INFO  13:56:20,062 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
WARN  13:56:20,101 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation 
INFO  13:56:20,236 GenomeAnalysisEngine - Preparing for traversal 
INFO  13:56:20,237 GenomeAnalysisEngine - Done preparing for traversal 
INFO  13:56:20,238 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  13:56:20,238 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  13:56:20,239 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
##### ERROR --
##### ERROR stack trace 
org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException: Unable to create iterator for rod named variant
    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.ManagingReferenceOrderedView.<init>(ManagingReferenceOrderedView.java:66)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:86)
    at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48)
    at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:98)
    at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:316)
    at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:123)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)
Caused by: java.lang.NumberFormatException: For input string: "1/1:255,255,0"
    at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
    at java.lang.Integer.parseInt(Integer.java:580)
    at java.lang.Integer.parseInt(Integer.java:615)
    at htsjdk.tribble.readers.TabixReader.getIntv(TabixReader.java:292)
    at htsjdk.tribble.readers.TabixReader.access$400(TabixReader.java:46)
    at htsjdk.tribble.readers.TabixReader$IteratorImpl.next(TabixReader.java:394)
    at htsjdk.tribble.readers.TabixIteratorLineReader.readLine(TabixIteratorLineReader.java:45)
    at htsjdk.tribble.TabixFeatureReader$FeatureIterator.readNextRecord(TabixFeatureReader.java:158)
    at htsjdk.tribble.TabixFeatureReader$FeatureIterator.<init>(TabixFeatureReader.java:146)
    at htsjdk.tribble.TabixFeatureReader.query(TabixFeatureReader.java:121)
    at org.broadinstitute.gatk.utils.refdata.tracks.RMDTrack.query(RMDTrack.java:119)
    at org.broadinstitute.gatk.engine.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:241)
    ... 12 more
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
##### 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 https://software.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Unable to create iterator for rod named variant
##### ERROR ------------------------------------------------------------------------------------------

SCRIPT:

#gatk FastaAlternateReferenceMaker w/ ambiguity codes
java -jar /opt/gatk/3.7.0/GenomeAnalysisTK.jar \
    --analysis_type FastaAlternateReferenceMaker \
    --reference_sequence /Users/****/NGS/bwa_sam_trial/OM_AN_FRAG_REF_FIN.fa \
    --out $home/bwa_sam_trial/fasta/fin/an85266_final.fasta \
    --variant $home/bwa_sam_trial/fasta/picard_renamed_an85266.vcf.gz \
    -IUPAC an85266

This error is cropping up but only for this one sample I am trying to run through my script. All the others seem to run through fine, but the final output FASTA file for this is extremely truncated to only 1/6 of the size it should be. I can't update either to see if there's something that could solve this issue in a newer version because the tool FastaAlternateReferenceMaker does not exist in GATK4 as of yet. Halp?

Post edited by Geraldine_VdAuwera on

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