Apollo is very slow with GFF3 track

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Francesco Cicconardi

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Mar 24, 2022, 11:56:45 AM3/24/22
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Hi,

I'm using Apollo with Docker. Loading a GFF3 file with 876k lines as a track makes the server extremely slow, if not stall.

Is there anything I can do to make it run faster?

I'm running it on an iMac
  Processor Name:        Quad-Core Intel Core i5
  Processor Speed:        3.8 GHz
  Number of Processors:        1
  Total Number of Cores:        4
  L2 Cache (per Core):        256 KB
  L3 Cache:        6 MB
  Memory:        32 GB

Thanks
F

Garrett Stevens

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Mar 24, 2022, 12:06:30 PM3/24/22
to Francesco Cicconardi, apollo
When you say you are loading a GFF3, do you mean that you are loading the GFF3 as annotations (e.g. using the CLI like "arrow annotations load_gff3")? Or are you opening the GFF3 as a track (e.g. "Tracks -> New Track" in the UI)? If you are opening it as a track, then you will want to use the "GFF3 Tabix" option instead. There is some information about how to index your GFF3 with Tabix here: https://jbrowse.org/docs/tutorial.html#loading-tabix-gff3.

Best,
Garrett

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Francesco Cicconardi

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Mar 24, 2022, 12:35:23 PM3/24/22
to apollo, stevens....@gmail.com, apollo, Francesco Cicconardi
Hi Stevens,

yes, GFF3 as a track (e.g. "Tracks -> New Track" in the UI). I followed the instruction but I got this:
Error: some feature reference other features that do exist in the file ...

:(
F

Garrett Stevens

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Mar 24, 2022, 12:47:32 PM3/24/22
to Francesco Cicconardi, apollo
You'll need to fix your GFF3 so it doesn't refer to features that don't exist. It looks like someone suggested a tool for fixing GFF3s to someone having a similar issue here: https://www.biostars.org/p/351556/#351619.

Best,
Garrett

Francesco Cicconardi

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Mar 24, 2022, 1:02:20 PM3/24/22
to Garrett Stevens, apollo
GFF3 format seems alright to me since it can be loaded as it is my many tools (IGV, gffread, CAT... you name it), it looks like something happens when it gets converted.
F

Francesco Cicconardi

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Mar 25, 2022, 11:02:34 AM3/25/22
to apollo, stevens....@gmail.com, apollo, Francesco Cicconardi
Hi Stevens,

I did a test, I download the gff3 of D. melanogaster, compressed it as you suggested and it returned no errors, but Apollo/jbrowse only shows transcripts with CDS and nothing which is not coding.
How is that possible?
Best,
F
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