[Gmod-ajax] ChunkSizeLimit errors with VCF files

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[Gmod-ajax] ChunkSizeLimit errors with VCF files

Jillian Rowe
Hello,

I recently updated to 1.11.4-dev from 1.11.0, and I am getting all kinds
of chunkSize errors with VCF files. We are mostly using JBrowse for VCF
files, so its really not useful unless this can be solved.

I have a VCF track from the 1K Genomes project. I think the default
chunkSizeLimit is 1,000,000.

Error: Too much data. Chunk size 1,482,784 bytes exceeds chunkSizeLimit
of 1,000,000.

So in the trackconfig I changed the chunkSizeLimit to 2000000.

Error: Too much data. Chunk size 2,228,548 bytes exceeds chunkSizeLimit
of 2,000,000.

Some of my other VCF tracks work. They are from smaller files than the
1K genomes files.

I also noticed JBrowse is MUCH slower, but I'm not sure if this is
something I've done or a change a within JBrowse.

This is my track config.

        {
             "label"         : "1kgenomes",
             "key"           : "1K Genomes",
             "storeClass"    : "JBrowse/Store/SeqFeature/VCFTabix",
             "urlTemplate"   :
"/genomes/1000genomes/{refseq}/ALL.{refseq}.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz",
             "tbiUrlTemplate":
"/genomes/1000genomes/{refseq}/ALL.{refseq}.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz.tbi",
             "type"          : "JBrowse/View/Track/HTMLVariants",
             "category" : "1000 Genomes Project",
         },

Thanks!

Best,
Jillian


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Re: ChunkSizeLimit errors with VCF files

Colin
This problem look like it's related to a known issue https://github.com/GMOD/jbrowse/issues/486

 Luckily it's been fixed and it will be appearing in the next release.  If you're interested in making a custom build with this included, i can follow up in the other thread.

-Colin


On Thu, Jul 24, 2014 at 5:48 AM, Jillian Rowe <[hidden email]> wrote:
Hello,

I recently updated to 1.11.4-dev from 1.11.0, and I am getting all kinds
of chunkSize errors with VCF files. We are mostly using JBrowse for VCF
files, so its really not useful unless this can be solved.

I have a VCF track from the 1K Genomes project. I think the default
chunkSizeLimit is 1,000,000.

Error: Too much data. Chunk size 1,482,784 bytes exceeds chunkSizeLimit
of 1,000,000.

So in the trackconfig I changed the chunkSizeLimit to 2000000.

Error: Too much data. Chunk size 2,228,548 bytes exceeds chunkSizeLimit
of 2,000,000.

Some of my other VCF tracks work. They are from smaller files than the
1K genomes files.

I also noticed JBrowse is MUCH slower, but I'm not sure if this is
something I've done or a change a within JBrowse.

This is my track config.

        {
             "label"         : "1kgenomes",
             "key"           : "1K Genomes",
             "storeClass"    : "JBrowse/Store/SeqFeature/VCFTabix",
             "urlTemplate"   :
"/genomes/1000genomes/{refseq}/ALL.{refseq}.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz",
             "tbiUrlTemplate":
"/genomes/1000genomes/{refseq}/ALL.{refseq}.phase1_release_v3.20101123.snps_indels_svs.genotypes.vcf.gz.tbi",
             "type"          : "JBrowse/View/Track/HTMLVariants",
             "category" : "1000 Genomes Project",
         },

Thanks!

Best,
Jillian


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search up to 200,000 lines of code with a free copy of Black Duck
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http://p.sf.net/sfu/bds
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