Closed philsteinberg closed 1 year ago
index_data.py
File does not exist in witness folder. That script generates index.json
, which is in the data folder. I copied index_data.py
from the PhyloWGS github into my local witness folder and ran it to re-generate the index.json
. That file is also an empty dictionary. When looking at the code in index_data.py
there seems to be an additional input .clusters.json
which we do not generate.
Error when running python2 -m SimpleHTTPServer
Serving HTTP on 0.0.0.0 port 8000 ...
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET / HTTP/1.1" 200 -
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 58464)
Traceback (most recent call last):
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 293, in _handle_request_noblock
self.process_request(request, client_address)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 321, in process_request
self.finish_request(request, client_address)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 334, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 657, in __init__
self.finish()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 716, in finish
self.wfile.close()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 283, in close
self.flush()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 307, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /css/dashboard.css HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /css/tree.css HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /js/stupidtable.min.js HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /js/state_manager.js HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:12] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:12] "GET /js/witness.js HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:13] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:13] "GET /favicon.ico HTTP/1.1" 404 -
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 58475)
Traceback (most recent call last):
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 293, in _handle_request_noblock
self.process_request(request, client_address)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 321, in process_request
self.finish_request(request, client_address)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 334, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 657, in __init__
self.finish()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 716, in finish
self.wfile.close()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 283, in close
self.flush()
File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 307, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------
127.0.0.1 - - [19/Dec/2022 09:36:16] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:16] "GET /js/stupidtable.min.js HTTP/1.1" 404 -
127.0.0.1 - - [19/Dec/2022 09:36:16] code 404, message File not found
127.0.0.1 - - [19/Dec/2022 09:36:16] "GET /js/state_manager.js HTTP/1.1" 404 -
I tried running it on the cluster and there it opens the window but there is no data loaded. Looking into past witness issues on the PhyloWGS github now.
python3 -m http.server
try this instead of python2 command
Example: Witness data for sample ILHNLNEV000008-T001-P01-F
and seed 97782
We create 2500 trees and choose the best tree (one that minimizes negative log likelihood (nlgLH))
Key & Interpretation:
Interpretation:
Sample ILHNLNEV000004-T001-P01-F
errored for some seeds. When visualizing this sample with seed 97782
all trees only have 2 nodes.
Sample ILHNLNEV000006-T001-P01-F
and seed 97782
PhyloWGS Result visualization: https://github.com/uclahs-cds/pipeline-call-SRC
TO-DO:
witness
folder to local device-muts.json
to.muts.json
and-summ.json
to.sum.json
(created a PR to in call-pipeline-SRC to fix this)index_data.py
to createindex.json