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higlass / higlass-docker

Builds a docker container wrapping higlass-server and higlass-client in nginx
MIT License
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Can not load and view the mcool file #173

Open yancychy opened 3 years ago

yancychy commented 3 years ago

Hi, I installed higlass-docker in my laptop. I have loaded and viewed some Hi-c mcool files before. But when I try to load another larger mcool files (>500M), it is not shown. The firebox told me to wait to load. I meet this problem before. It will cost a long time (several days) to wait and veiw the Hi-c data by change. I am not sure how to fix this problem. Refresh the webpage dosenot help. Thanks.

pkerpedjiev commented 3 years ago

Hi, is the file you're trying to load public by chance?

Can you paste the command that you used to load it?

yancychy commented 3 years ago

Thanks. I just load into my local web server in the docker image. https://drive.google.com/file/d/1X357S1JQuKrWK1U0ilzu76bc1lzWvA7R/view?usp=sharing https://drive.google.com/file/d/1Pof35IhV77WLZEuUMsi6TCthiPhKyXq7/view?usp=sharing Command is: docker pull higlass/higlass-docker:v0.6.1 # higher versions are experimental and may or may not work docker run --detach --publish 8989:80 --volume ~/hg-data:/data --volume ~/tmp:/tmp --name higlass-container -e SITE_URL=my.higlass.org higlass/higlass-docker:v0.6.1 docker exec higlass-container python higlass-server/manage.py ingest_tileset --filename /tmp/GSE80701_DpnII_HinfI_combo250.mcool --filetype cooler --datatype matrix

pkerpedjiev commented 3 years ago

That's odd. Could you open up the browser console and take a screenshot?

On chrome you can open the console from chrome menu -> more tools -> developer tools. The select the 'Console' tab.

yancychy commented 3 years ago

https://drive.google.com/file/d/16m_6wsA2u8JXn5qEE1Scg35Mw4NltOgw/view?usp=sharing Thanks. I changed to my previous mcool file. It works now. GSE80701_DpnII_HinfI_combo250.mcool is coverted from the hic file. Maybe there are some error in the GSE80701_DpnII_HinfI_combo250.mcool.

pkerpedjiev commented 3 years ago

Oh, yeah it looks like the lowest resolution in that file is still very detailed which causes higlass to try to load too many tiles. In order to avoid crashing your browser it only loads a very small subset of them so you don't see anything. If you zoom in you should be able to see details.

You may be able to run cooler zoomify on that file to get a more reasonable set of resolutions but I'm not sure how well that works on a file with many resolutions already.

yancychy commented 3 years ago

Thanks, I used cooler zoomify the produce the mcool file. Maybe my laptop is not so fast to load the data.