File not found trackData.jsonz

[Michał T. Lorenc]

Hi all,

I uploaded the following GFF3 file via Apollo's "New track" button:

$ ls -hlatr

-rw-r----- 1 debian debian 2.0G Jul 12 00:50 LabUsa16cWild01-20_C-N_snp.gff3

$ head LabUsa16cWild01-20_C-N_snp.gff3
##gff-version 3
NbLab360C00 SGSautoSNP SNP 121 121 . . . Name=NbLab3600000001;ID=NbLab3600000001;Contig name=NbLab360C00;SNP score=19;SNP pos. on scaffold=121;Genotype C=10*G;Genotype L=45*G;Genotype N=19*T;Genotype Q=23*G;Genotype S=82*G;Genotype T=18*G;Genotype U=54*G;Genotype W=24*G;Changes=G/T
NbLab360C00 SGSautoSNP SNP 409 409 . . . Name=NbLab3600000002;ID=NbLab3600000002;Contig name=NbLab360C00;SNP score=44;SNP pos. on scaffold=409;Genotype C=17*T;Genotype L=59*T;Genotype N=44*C;Genotype Q=54*T;Genotype S=106*T;Genotype T=41*T;Genotype U=95*T;Genotype W=51*T;Changes=C/T
NbLab360C00 SGSautoSNP SNP 519 519 . . . Name=NbLab3600000003;ID=NbLab3600000003;Contig name=NbLab360C00;SNP score=49;SNP pos. on scaffold=519;Genotype C=27*T;Genotype L=79*T;Genotype N=49*C;Genotype Q=63*T;Genotype S=105*T;Genotype T=55*T;Genotype U=99*T;Genotype W=77*T;Changes=C/T

However, the "16c vs LAB SNPs" worked fine but "16c vs NWA SNPs." does not load any content and the looks show this error:

2022-07-12 02:27:56,201 [http-nio-8080-exec-66] ERROR apollo.JbrowseController  - File not found: /data/apollo_data/3135830-LAB360/tracks/16c_vs_NWA_SNPs/NbLab360C17/trackData.jsonz

Are there any file size restrictions for uploading via GUI?

Thank you in advance,

Michal

[Nathan Dunn]

There are upload limits.  By default, they are pretty large (2 or 4 GBs?). 

What “type” of track are you using (JSON I’m assuming?)?

It might be worth just trying to do it by hand with flatfile-to-json.pl from JBrowse to see if you get any errors for those tracks.  

Nathan

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[Nathan Dunn]

It was probably an error on processing the file.  

Also, I’m not sure if it would know what to do with SNP types by default. 

Conversely, I would just convert them to VCF files and upload them that way as I think the visualization would be more meaningful, though hopefully you have an existing VCF file you can pull from:

  

You could try updating the top type to “SNP”:

Nathan

On Jul 14, 2022, at 7:25 PM, Michał T. Lorenc <m.t.l...@gmail.com> wrote:

Yes, Gff3 JSON.

[Michał T. Lorenc]

Hi all,

It worked the whole time, but it took a long time. I solved the problem by compressing and indexing the files.

Best wishes,

Michal