GFF size limit

[biouserPD]

Hi,
I tried to open a GFF file in the jbrowse2 desktop version 1.5.1...the file is about 3.6gb and the program showed us the following error: "Range error:file size (364....)is greater than 2 GB." Is it possible to expand the memory limit of the program?
Or do you suggest other solutions?
Thanks a lot
M

[cmdcolin]

Good question. There are some current limits to opening large GFF (there is actually a limit of around ~512MB which we give an error for but apparently there is a separate other issue for bigger than 2GB)

I would suggest making a tabix index for your GFF

To do so, see https://jbrowse.org/jb2/docs/superquickstart_web/#loading-gff3

Basically

sudo apt install genometools # or install http://genometools.org/ some other way of interest
gt gff3 -sortlines -tidy -retainids yourfile.gff > yourfile.sorted.gff
bgzip yourfile.sorted.gff
tabix yourfile.sorted.gff.gz

You can skip the part where you use jbrowse add-track if using the desktop version. This produces

yourfile.sorted.gff.gz and yourfile.sorted.gff.gz.tbi

And you can open this up in the "Add track" workflow

We may end up making a workflow inside jbrowse desktop to perform tabix indexing on the fly so that it is easier to open large files! Let me know if this helps

[biouserPD]

Hi,
thanks a lot for your help. I tried your suggestion and I was able to upload the GFF file in Jbrowse.