Question: JBrowse help with opening a Gff gene model file
gravatar for Hwaterma
6 weeks ago by
Hwaterma0 wrote:

I am trying to look at my gene model on JBrowse and keep getting "an error was encountered when displaying this track. Diagnostic message: [object ProgressEvent]". I can't seem to find what it mean anywhere. Can someone please help?

jbrowse • 135 views
ADD COMMENTlink modified 5 weeks ago by Biostar ♦♦ 20 • written 6 weeks ago by Hwaterma0

Can you try converting the GFF3 into a json track and see what would happen? That may give you more information if anything goes wrong. Also, it is usually useful to run a GFF3 check using gff_validator, even though your GFF3 seems to be fine.

ADD REPLYlink written 5 weeks ago by Vitis2.2k

I am presuming you mean convert to json using bin/ --gff yourfile.gff --trackLabel. Just wanted to clarify that in case it was unclear for Hwaterma

ADD REPLYlink written 5 weeks ago by cmdcolin1.2k

Thanks for clarifying that for me!

ADD REPLYlink written 5 weeks ago by Vitis2.2k

Hi Hwaterma, I'm a JBrowse dev. It is hard to debug this without more info. If you can share any more data or info about your setup let me know

ADD REPLYlink written 6 weeks ago by cmdcolin1.2k

Here is the top of my GFF file:

##gff-version 3
utg002023l_pilon    .   contig  1   648515  .   .   .   ID=utg002023l_pilon;Name=utg002023l_pilon
utg002023l_pilon    maker   gene    52467   53191   .   +   .   ID=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1;Name=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1
utg002023l_pilon    maker   mRNA    52467   53191   405 +   .   ID=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1;Parent=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1;Name=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1;_AED=0.24;_eAED=0.27;_QI=0|1|0|1|0|0|2|0|134
utg002023l_pilon    maker   exon    52467   52596   .   +   .   ID=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1:exon:36371;Parent=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1
utg002023l_pilon    maker   exon    52917   53191   .   +   .   ID=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1:exon:36372;Parent=maker-utg002023l_pilon-exonerate_protein2genome-gene-0.1-mRNA-1
ADD REPLYlink modified 5 weeks ago by ATpoint19k • written 6 weeks ago by Hwaterma0

How is this track opened? Did you use the Track->Open track inside JBrowse or loaded via command line? Also the formatting on this gff is messed up by posting so it's hard to tell if it's formatted right, but a cursory look appears to not have anything wrong

ADD REPLYlink written 6 weeks ago by cmdcolin1.2k

I am on the online JBrowse and I click on Track. That opens a pull down menu. Then I click on open track file or URL. The it make a track for me but says the error instead of my info.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Hwaterma0

What browser are you using? I do not get any error doing this in a local instance

ADD REPLYlink written 4 weeks ago by cmdcolin1.2k
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