Error loading gff3

[mtr...@mindspring.com]

Hello

When attempting to open the following session file in IGV (v. 2.5.3)

 

<?xml version="1.0" encoding="UTF-8"?>
<Global> genome="MIR604_FS_IS_FS.fa" locus="MIR604_FS_IS_FS.fa" version="3"
<Resources>
<Resource name="low complexity" path="http://demeter//scratch-large/1-daily/TrEC-SIPB/1564580075/MIR604_FS_IS_FS.fa-1564580075-low_complexity.bedgraph"/>
<Resource name="homopolymers" path="http://demeter//scratch-large/1-daily/TrEC-SIPB/1564580075/MIR604_FS_IS_FS.fa-1564580075-homopolymers.bedgraph"/>
<Resource name="arrow variants" path="http://demeter//scratch-large/1-daily/TrEC-SIPB/1564580075/Zma-B-S1-47K15_MIR604.bam-vs-MIR604_FS_IS_FS.fa.1564580075.blasr.sort.arrow.gff3"/>
</Resources>
</Global>

I get the following error (Note both the "low complexity" and "homopolymer tracks loaded correctly)

Errors were encountered loading the session: http://demeter//scratch-large/1-daily/TrEC-SIPB/1564580075/Zma-B-S1-47K15_MIR604.bam-vs-MIR604_FS_IS_FS.fa.1564580075.blasr.sort.arrow.gff3   org.broad.igv.exceptions.DataLoadException: Unable to read index file, for input source: http://demeter//scratch-large/1-daily/TrEC-SIPB/1564580075/Zma-B-S1-47K15_MIR604.bam-vs-MIR604_FS_IS_FS.fa.1564580075.blasr.sort.arrow.gff3

The gff3 file is 

##gff-version 3
##pacbio-variant-version 2.1
##date Wed Jul 31 09:34:54 2019
##feature-ontology http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12
##source GenomicConsensus 2.2.2
##source-commandline /thirdparty/smrtanalysis/6.0.0/install/smrtlink-release_6.0.0.47841/bundles/smrttools/install/smrttools-release_6.0.0.47835/private/pacbio/pythonpkgs/GenomicConsensus/binwrap/../../../../../private/pacbio/pythonpkgs/GenomicConsensus/bin/variantCaller --algorithm arrow --log-file variantCaller.log -r MIR604_FS_IS_FS.fa -o Zma-B-S1-47K15_MIR604.bam-vs-MIR604_FS_IS_FS.fa.1564580075.blasr.sort.arrow.vcf -o Zma-B-S1-47K15_MIR604.bam-vs-MIR604_FS_IS_FS.fa.1564580075.blasr.sort.arrow.gff -o Zma-B-S1-47K15_MIR604.bam-vs-MIR604_FS_IS_FS.fa.1564580075.blasr.sort.fastq --debug --reportEffectiveCoverage --minMapQV 40 Zma-B-S1-47K15_MIR604.bam-vs-MIR604_FS_IS_FS.fa.1564580075.blasr.sort.bam
##source-alignment-file /scratch-large/1-daily/TrEC-SIPB/1564580075/Zma-B-S1-47K15_MIR604.bam-vs-MIR604_FS_IS_FS.fa.1564580075.blasr.sort.bam
##source-reference-file /scratch-large/1-daily/TrEC-SIPB/1564580075/MIR604_FS_IS_FS.fa
##sequence-region MIR604_FS_IS_FS 1 11632
MIR604_FS_IS_FS .       insertion       608     608     .       .       .       reference=.;variantSeq=A;coverage=100;confidence=93;effectiveCoverage=83

What is wrong here?  What index file is the error referring to?

Thanks for your help

Mark 

[James Robinson]

This appears to be caused by a bug in a library we use, the htsjdk.   I'm unsure when this problem was introduced.   I'm working on a fix,  in the meantime the only workaround would be to create a "tribble index" for the gff3 file using igv or igvtools.

I expect to have a fix released by the end of the week.

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[mtr...@mindspring.com]

Thanks for looking into this.  Please let me know when you apply the patch.

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[James Robinson]

This should be fixed now,  release is 2.6.2

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