HiGlass browser very slow

[rahmas36]

Hi, I have noticed that HiGlass is running slow these days. I used to be able to navigate smoothly before. What could be the reason?

[pkerpedjiev]

Hard to say. Would you be willing to share a viewconf that is particularly slow?

[pkerpedjiev]

Also, what browser are you using?

[rahmas36]

I am using chrome. Here are some snapshots to show how the matrices are not loading properly.

[pkerpedjiev]

Where is the data coming form? Can you share the cooler file?

[rahmas36]

https://drive.google.com/file/d/1dnP5gy-I0jP8cYy2dW1BVY0K9tnOaeuU/view?usp=sharing, https://drive.google.com/file/d/1nWjiTk0H7PfbffHXo6Rj0IHLwjyOdTpX/view?usp=sharing
Here are the mcool files I was trying to browse.

[rahmas36]

Hi, were you able to detect any problems with the files? Could it be that I don't have enough memory to run docker?

[pkerpedjiev]

Hi, sorry, I hadn't been able to look. I just looked at your cooler files and it looks like they're for the human genome but the largest resolution is 2.5M. That means that at the lowest resolution, you'll need 25 tiles to display the entire genome. May I suggest adding 5M and 10M resolutions and trying again?

It also looks like you have chrM as the first chromosome. There's no inherent problem with that but most other datasets (namely gene annotations) are ordered 1,2,3...,X,Y,M. This means your gene annotations won't match your cooler files. If it's a possibility, I would recommend reordering your chromosomes to the correct ordering.

For both of the tasks I suggested there should be cooler commands to accomplish. Unfortunately I'm not sure what they are off the top of my head. If you can't find them, open an issue there or pop into the Open2C slack and ask there.

[Naveen-Ahuja]

Hello,

I am facing a similar problem, where HiGlass is just stuck at loading my file.

Here is a link to my 5Mb resolution matrix:
https://drive.google.com/drive/folders/11UHdLeO-E7EMR4jJJ7x-p70oq8aM_7Jv?usp=sharing

Could you please let me know how I can fix this?

Thank you

[pkerpedjiev]

Requested access to the file.

[Naveen-Ahuja]

access granted

[pkerpedjiev]

Here's the error I get when loading it:

    self.raise_uncaught_exception(exc)
  File "/usr/local/lib/python3.8/dist-packages/rest_framework/views.py", line 476, in raise_uncaught_exception
    raise exc
  File "/usr/local/lib/python3.8/dist-packages/rest_framework/views.py", line 502, in dispatch
    response = handler(request, *args, **kwargs)
  File "/usr/local/lib/python3.8/dist-packages/rest_framework/decorators.py", line 50, in handler
    return func(*args, **kwargs)
  File "/home/higlass/projects/higlass-server/./tilesets/views.py", line 696, in tileset_info
    tileset_infos[tileset_uuid] = hgco.tileset_info(
  File "/usr/local/lib/python3.8/dist-packages/clodius/tiles/cooler.py", line 545, in tileset_info
    (f, info) = make_mats(filepath)
  File "/usr/local/lib/python3.8/dist-packages/clodius/tiles/cooler.py", line 508, in make_mats
    info = _get_info_multi_v1(filepath)
  File "/usr/local/lib/python3.8/dist-packages/clodius/tiles/cooler.py", line 179, in _get_info_multi_v1
    raise ValueError("The `max_zoom` attribute is missing.")
ValueError: The `max_zoom` attribute is missing.

How did you create that file? Did you use the latest version of cooler?

[Naveen-Ahuja]

The file was originallly in .hic pro format, so a matrix and bed file. I then loaded it into HiCexplorer converted it to .h5 to bin and correct using ICE at 5Mb, then I converted it to .mcool /.cool

[pkerpedjiev]

@Naveen-Ahuja can you check which version of cooler you're using?

cooler --version

@nvictus do you know if the latest version of cooler adds the max_zoom attribute?

[Naveen-Ahuja]

cooler, version 0.9.1

[pkerpedjiev]

Do you think you could send me the original .cool file and I can try converting and loading?

[Naveen-Ahuja]

The file was originally in .hic pro format, so a matrix and bed file. Would you like me to send you that?

I then loaded it into HiCexplorer converted it to .h5 to bin and corrected using ICE at 5Mb, then I converted it to .mcool /.cool

I added the .cool file also in the googledrive link I shared above

[pkerpedjiev]

Try doing this on your .cool file:

mv HGPS_P7_5Mb_ice.mcool HGPS_P7_5Mb_ice.mcool.bak
cooler zoomify HGPS_P7_5Mb_ice.cool

That will create a new .mcool file with the correct metadata for viewing in higlass. Just tried it and it worked.

[Naveen-Ahuja]

Yes! It worked. Thank you very much.

Just out of curiosity, could you explain to me what the issue was and how the commands you shared above solved it?

Thanks

[pkerpedjiev]

I suspect that you hadn't made the file multires and that's why it was missing the max_zoom attribute. cooler zoomify adds zoom information to a regular cooler and makes it viewable in higlass.

[Naveen-Ahuja]

Oh I see, thank you for the quick responses!