Closed shaodongyan closed 1 year ago
nickjcroucher
commented
1 year ago If you download this file with curl -o /public/home/s20203050772/miniconda3/envs/poppunk/lib/python3.10/site-packages/PopPUNK/data/microreact_example.pkl https://github.com/bacpop/PopPUNK/blob/master/PopPUNK/data/microreact_example.pkl, does that resolve thew issue?
shaodongyan
commented
1 year ago If you download this file with
curl -o /public/home/s20203050772/miniconda3/envs/poppunk/lib/python3.10/site-packages/PopPUNK/data/microreact_example.pkl https://github.com/bacpop/PopPUNK/blob/master/PopPUNK/data/microreact_example.pkl, does that resolve thew issue?
Thanks！ That resolve thew issue！
shaodongyan
commented
1 year ago Sorry, But I need more help , I fit a model with K=7, but I visualise this model ,it has cluster more than 7, How can i solve it ?thanks!
shaodongyan
commented
1 year ago 
Two things can't match
shaodongyan
commented
1 year ago 
shaodongyan
commented
1 year ago I launch a new issue . Close it
Versions poppunk 2.5.0
Command used and output returned Firstly, I used "poppunk_assign --db /public/home/s20203050772/database/popunk/e_coli_poppunk --query qfile.tsv \ --output poppunk_clusters_new --threads 56 --update-db" Secondly,I used " poppunk_visualise --ref-db poppunk_clusters_new/ --tree both --microreact --output dense_mst_viz".
Describe the bug But , I did it with Graph-tools OpenMP parallelisation enabled: with 1 threads PopPUNK: visualise Loading previously refined model Completed model loading Generating MST from dense distances (may be slow) Starting calculation of minimum-spanning tree Completed calculation of minimum-spanning tree Drawing MST Building phylogeny Writing microreact output Parsed data, now writing to CSV Running mandrake Running on CPU Preprocessing 10800 samples with perplexity = 20 took 44122ms Optimizing Progress: 99.9%, eta=0.0010, Eq=0.9650969196, clashes=0.0% Optimizing done in 0s Traceback (most recent call last): File "/public/home/s20203050772/miniconda3/envs/poppunk/bin/poppunk_visualise", line 11, in
sys.exit(main())
File "/public/home/s20203050772/miniconda3/envs/poppunk/lib/python3.10/site-packages/PopPUNK/visualise.py", line 624, in main
generate_visualisations(args.query_db,
File "/public/home/s20203050772/miniconda3/envs/poppunk/lib/python3.10/site-packages/PopPUNK/visualise.py", line 561, in generate_visualisations
url = createMicroreact(output, microreact_files, api_key)
File "/public/home/s20203050772/miniconda3/envs/poppunk/lib/python3.10/site-packages/PopPUNK/plot.py", line 779, in createMicroreact
with pkg_resources.resource_stream(name, 'data/microreact_example.pkl') as example_pickle:
File "/public/home/s20203050772/miniconda3/envs/poppunk/lib/python3.10/site-packages/pkg_resources/init.py", line 1160, in resource_stream
return get_provider(package_or_requirement).get_resource_stream(
File "/public/home/s20203050772/miniconda3/envs/poppunk/lib/python3.10/site-packages/pkg_resources/init.py", line 1632, in get_resource_stream
return open(self._fn(self.module_path, resource_name), 'rb')
FileNotFoundError: [Errno 2] 没有那个文件或目录: '/public/home/s20203050772/miniconda3/envs/poppunk/lib/python3.10/site-packages/PopPUNK/data/microreact_example.pkl'
Please Help me,Thanks!