running error on local machine
FAVITES Version
latest (Feb 13th, 2018 )
Environment
Mac OS
Configuration File
Unexpected Behavior
{
"ContactNetwork": "NetworkX",
"ContactNetworkGenerator": "RandonPartitionGraph",
"Driver": "Default",
"EndCriteria": "GEMF",
"Logging": "File",
"NodeAvailability": "Perfect",
"NodeEvolution": "None",
"NumBranchSample": "Single",
"NumTimeSample": "Once",
"SeedSelection": "Random",
"SeedSequence": "Random",
"SequenceEvolution": "NoMutation",
"seed_sequence_length": 1,
"Sequencing": "Perfect",
"SourceSample": "Random",
"TimeSample": "End",
"TransmissionNodeSample": "GEMF",
"TransmissionTimeSample": "HIVARTGranichGEMF",
"TreeNode": "Simple",
"TreeUnit": "LogNormal",
"end_time": 70,
"rpg_sizes": [20,20,20],
"rpg_p_in": 0.1,
"rpg_p_out": 0.002,
"d_or_u": "u",
"gemf_path": "GEMF",
"grinder_path": "grinder",
"hiv_a1_to_a2": 4.333333333333333,
"hiv_a1_to_d": 0,
"hiv_a1_to_i1": 0.48,
"hiv_a2_to_a3": 0,
"hiv_a2_to_d": 0,
"hiv_a2_to_i2": 0.48,
"hiv_a3_to_a4": 0,
"hiv_a3_to_d": 0,
"hiv_a3_to_i3": 0,
"hiv_a4_to_d": 0,
"hiv_a4_to_i4": 0,
"hiv_i1_to_a1": 0.5,
"hiv_i1_to_d": 0,
"hiv_i1_to_i2": 8.666666666666666,
"hiv_i2_to_a2": 0.5,
"hiv_i2_to_d": 0,
"hiv_i2_to_i3": 0,
"hiv_i3_to_a3": 0,
"hiv_i3_to_d": 0,
"hiv_i3_to_i4": 0,
"hiv_i4_to_a4": 0,
"hiv_i4_to_d": 0,
"hiv_ns_to_d": 0,
"hiv_ns_to_s": 999999,
"hiv_s_to_d": 0,
"hiv_s_to_i1_by_a1": 0.005625,
"hiv_s_to_i1_by_a2": 0,
"hiv_s_to_i1_by_a3": 0,
"hiv_s_to_i1_by_a4": 0,
"hiv_s_to_i1_by_i1": 0.25,
"hiv_s_to_i1_by_i2": 0.05,
"hiv_s_to_i1_by_i3": 0,
"hiv_s_to_i1_by_i4": 0,
"hiv_s_to_i1_seed": 0,
"hmmemit_path": "hmmemit",
"java_path": "java",
"num_seeds": 1,
"nw_rename_path": "nw_rename",
"out_dir": "FAVITES_output_test3",
"seed_population": 20,
"seqgen_a_to_c": 1.765707,
"seqgen_a_to_g": 9.587649,
"seqgen_a_to_t": 0.691915,
"seqgen_c_to_g": 0.863348,
"seqgen_c_to_t": 10.282617,
"seqgen_freq_a": 0.392,
"seqgen_freq_c": 0.165,
"seqgen_freq_g": 0.212,
"seqgen_freq_t": 0.232,
"seqgen_g_to_t": 1.0,
"seqgen_gamma_shape": 0.405129,
"seqgen_num_gamma_rate_categories": "",
"seqgen_path": "seq-gen",
"tree_rate_mean": -5.5,
"tree_rate_stdev": 0.2,
"viral_sequence_type": "HIV1-B-DNA-POL-LITTLE",
"vts_growthRate": 2.851904,
"vts_model": "logistic",
"vts_n0": 1,
"vts_t50": -2,
"num_cn_nodes" "100"
"ws_k" "3"
"ws_prob" "0.02"
"PostValidation": "Dummy"
}
run_favites_docker.py -c Config-small-rp.json -u -v
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 1316, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1230, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1276, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1225, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1017, in _send_output
self.send(msg)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 955, in send
self.connect()
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1391, in connect
server_hostname=server_hostname)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py", line 410, in wrap_socket
_session=session
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py", line 821, in init
self.do_handshake()
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py", line 1075, in do_handshake
self._sslobj.do_handshake()
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/ssl.py", line 696, in do_handshake
self._sslobj.do_handshake()
ssl.SSLCertVerificationError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:864)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/bin/run_favites_docker.py", line 11, in
DOCKER_LATEST_TAG = sorted([t for t in urlopen("https://hub.docker.com/r/%s/tags/"%DOCKER_IMAGE).read().decode('utf-8').split('"tags":')[1].split(':')[-1][1:-2].replace('"','').split(',') if '.' in t])[-1]
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 1359, in https_open
context=self._context, check_hostname=self._check_hostname)
File "/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py", line 1318, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:864)>