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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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Error retrieving tilesetInfo from: /api/v1 #159

Open JiangXu123 opened 4 years ago

JiangXu123 commented 4 years ago

Hey guys, I was following the introduction on how to set up the local Higlass and got it run with the example dataset in the tutorial of Higlass docker: https://github.com/higlass/higlass-docker However, when I tried to load my own dataset to Higlass, I encountered the error message as shown in the title of this post.
I also went back to the terminal end to see what happened, I found if I ingest the data in the tutorial, when I use the curl command to retrieve the information, it works well. But if I ingest my own data and tried to find the information with the curl command, I also encounter another error. here is the detail: jiangxu$ curl http://localhost:8888/api/v1/tilesets/ {"count":2,"next":null,"previous":null,"results":[{"uuid":"JSjAlQH2QB6g_amkwsCpBQ","datafile":"http://localhost:8888/api/v1/tilesets/media/uploads/CTCC_SDS_HindIII_10k_balanced_sorted_HeRuS8m.cool","filetype":"cooler","datatype":"matrix","name":"CTCC_SDS_HindIII_10k_balanced_sorted.cool","coordSystem":"","coordSystem2":"","created":"2019-11-15T13:51:29.603898Z","project":"U_mj54GkTB2tCtZ1UxeNNQ","project_name":"","description":"","private":false},{"uuid":"HvoNHOapQBiWVQ02hxA3Zw","datafile":"http://localhost:8888/api/v1/tilesets/media/uploads/dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires_jlfN230.cool","filetype":"cooler","datatype":"matrix","name":"dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool","coordSystem":"","coordSystem2":"","created":"2019-11-15T14:00:22.264898Z","project":"U_mj54GkTB2tCtZ1UxeNNQ","project_name":"","description":"","private":false}]}(base) Jiangs-MacBook-Pro:hg-tmp jiangxu$ curl http://localhost:8888/api/v1/tileset_info/?d=HvoNHOapQBiWVQ02hxA3Zw {"HvoNHOapQBiWVQ02hxA3Zw": {"min_pos": [0, 0], "max_pos": [3095693983, 3095693983], "max_zoom": 4, "max_width": 4096000000, "bins_per_dimension": 256, "transforms": [{"name": "ICE", "value": "weight"}], "chromsizes": [["chr1", 249250621], ["chr2", 243199373], ["chr3", 198022430], ["chr4", 191154276], ["chr5", 180915260], ["chr6", 171115067], ["chr7", 159138663], ["chr8", 146364022], ["chr9", 141213431], ["chr10", 135534747], ["chr11", 135006516], ["chr12", 133851895], ["chr13", 115169878], ["chr14", 107349540], ["chr15", 102531392], ["chr16", 90354753], ["chr17", 81195210], ["chr18", 78077248], ["chr19", 59128983], ["chr20", 63025520], ["chr21", 48129895], ["chr22", 51304566], ["chrX", 155270560], ["chrY", 59373566], ["chrM", 16571]], "name": "dixon2012-h1hesc-hindiii-allreps-filtered.1000kb.multires.cool", "datatype": "matrix", "coordSystem": "", "coordSystem2": ""}}(base) Jiangs-MacBook-Pro:hg-tmp jiangxu$ curl http://localhost:8888/api/v1/tileset_info/?d=JSjAlQH2QB6g_amkwsCpBQ

Server Error (500)

(base) Jiangs-MacBook-Pro:hg-tmp jiangxu$ The data set I encountered the error was generated from the 'cooler cload pairix' of the cooler package. Could you guys help me to solve the problem. Thank you! Best! Jiang
pkerpedjiev commented 4 years ago

Hi Jiang

I suspect you need to run cooler zoomify after cooler cload pairix: https://docs.higlass.io/data_preparation.html#zoomify

To further diagnose the error though, could you paste the last 30 or so lines from ~/hg-data/log/hgs.log? (Replace ~/hg-data with your higlass data directory).

JiangXu123 commented 4 years ago

Hi pkerpedjiev, I will redo the cooler zoomify as you suggested. And below is the contents of the log: [15/Nov/2019 14:10:09] ERROR [django.request:228] Internal Server Error: /api/v1/tileset_info/ Traceback (most recent call last): File "/opt/conda/lib/python3.6/site-packages/django/core/handlers/exception.py", line 34, in inner response = get_response(request) File "/opt/conda/lib/python3.6/site-packages/django/core/handlers/base.py", line 126, in _get_response response = self.process_exception_by_middleware(e, request) File "/opt/conda/lib/python3.6/site-packages/django/core/handlers/base.py", line 124, in _get_response response = wrapped_callback(request, *callback_args, callback_kwargs) File "/opt/conda/lib/python3.6/site-packages/django/views/decorators/csrf.py", line 54, in wrapped_view return view_func(*args, *kwargs) File "/opt/conda/lib/python3.6/site-packages/django/views/generic/base.py", line 68, in view return self.dispatch(request, args, kwargs) File "/opt/conda/lib/python3.6/site-packages/rest_framework/views.py", line 495, in dispatch response = self.handle_exception(exc) File "/opt/conda/lib/python3.6/site-packages/rest_framework/views.py", line 455, in handle_exception self.raise_uncaught_exception(exc) File "/opt/conda/lib/python3.6/site-packages/rest_framework/views.py", line 492, in dispatch response = handler(request, *args, *kwargs) File "/opt/conda/lib/python3.6/site-packages/rest_framework/decorators.py", line 54, in handler return func(args, **kwargs) File "./tilesets/views.py", line 609, in tileset_info tileset_object.datafile.path File "/opt/conda/lib/python3.6/site-packages/clodius/tiles/cooler.py", line 535, in tileset_info (f, info) = make_mats(filepath) File "/opt/conda/lib/python3.6/site-packages/clodius/tiles/cooler.py", line 498, in make_mats info = _get_info_multi_v1(filepath) File "/opt/conda/lib/python3.6/site-packages/clodius/tiles/cooler.py", line 178, in _get_info_multi_v1 'The max_zoom attribute is missing.' ValueError: The max_zoom attribute is missing.

JiangXu123 commented 4 years ago

Hi pkerpedjiev, I tried the 'zoomified' cool file and it works. I have a question, is the mcool file a required format for Higlass? Thanks.

pkerpedjiev commented 4 years ago

Yes, the mcool file is a "multi-resolution" cooler file. It's just a collection of individual coolers calculated at different resolutions (e.g. 1K, 2K, 5K, 10K, 25K...). This is what makes it possible for higlass to zoom in across multiple orders of magnitude of resolution.