msbio run error #1
Description
I get the following error when running msbio. I ran on ubuntu 20.04 and
Docker version 20.10.14, build a224086349
I followed the instructions from https://metascape.org/gp/index.html#/menu/msbio
bin/up.sh && bin/ms.sh -u -o /data/output_single_id_txt /data/example/single_list_id.txt
And got the error message below. I tried to open port 1234 but this did not work. I would be grateful for help.
Metascape for Bioinformaticians (academic version)
Version: v3.5.20220101
Licensee: christofer.karlsson@med.lu.se
Expiration: 2023-07-15
START> job #1, input=/data/example/single_list_id.txt, output=/data/output_single_id_txt
MetaEngine> Start timer ...
MetaEngine::analysis> Start timer ...
output_single_id_txt:739|MetaEngine> Passed: 0.1 secs, Membership
output_single_id_txt:739|MetaEngine> Passed: 0.0 secs, genelists_overlap_analysis
output_single_id_txt:739|MetaEngine::analysis> Passed: 0.0 secs, ******* OVERLAP
Loading Entrez gene table for 9606...
Loading mapping table for 9606...
Load GPDB GO database for tax_id: 9606 ...
GeneLists::go_analysis> Start timer ...
output_single_id_txt:739|MetaEngine> Passed: 16.7 secs, GO membership: t_go_mem 191 x 7
output_single_id_txt:739|MetaEngine> Passed: 0.0 secs, GO Enrichment
output_single_id_txt:739|MetaEngine::analysis> Passed: 16.7 secs, ***** GO ANALYSIS
> Start timer ...
output_single_id_txt:739|> Passed: 19.3 secs, data loaded from /home/meta_test/mylib/STRING/Interaction.9606.csv.gz
output_single_id_txt:739|> Passed: 0.9 secs, Start processing each tax_id
output_single_id_txt:739|> Passed: 9.5 secs, processed :9606
PPI databases loaded
output_single_id_txt:739|MetaEngine> Passed: 30.0 secs, Start PPI Analysis
GeneList::ppi_analysis> Start timer ...
Size of total network: 86
Find MCODE components ...
Found 4 MCODE components
output_single_id_txt:739|GeneList::ppi_analysis> Passed: 1.5 secs, Network DONE
output_single_id_txt:739|MetaEngine::analysis> Passed: 31.5 secs, ***** PPI ANALYSIS
Final Weights: [1. 1. 1.]
output_single_id_txt:739|MetaEngine::analysis> Passed: 0.0 secs, ***** EVIDENCE
MetaEngine::GPEC_go_analysis> Start timer ...
GO_Cluster> Start timer ...
output_single_id_txt:739|GO_Cluster> Passed: 1.3 secs, Done membership...
GO_Cluster::cluster> Start timer ...
Matrix size: 91 genes x 191 GOs
output_single_id_txt:739|GO_Cluster::cluster> Passed: 1.1 secs, Kappa done ...
GOList::membership> Start timer ...
output_single_id_txt:739|GOList::membership> Passed: 0.0 secs, Score calculation
output_single_id_txt:739|GOList::membership> Passed: 0.0 secs, Get membership matrix
output_single_id_txt:739|GOList::membership> Passed: 1.8 secs, Cluster genes and columns for each cluster.
Add node count ...
output_single_id_txt:739|MetaEngine::analysis> Passed: 7.9 secs, ****** GPEC GO
MetaEngine::GPEC_ppi_analysis> Start timer ...
output_single_id_txt:739|MetaEngine::GPEC_ppi_analysis> Passed: 0.0 secs, ***Start GO Analysis***
output_single_id_txt:739|MetaEngine::GPEC_ppi_analysis> Passed: 2.7 secs, Finish GO analysis
output_single_id_txt:739|MetaEngine::GPEC_ppi_analysis> Passed: 0.1 secs, *****GO Analysis within PPI Analysis
output_single_id_txt:739|MetaEngine::analysis> Passed: 2.8 secs, ****** GPEC PPI
qc_analysis: [34, 35, 36, 200, 7]
GeneLists::go_analysis> Start timer ...
output_single_id_txt:739|MetaEngine> Passed: 14.2 secs, GO membership: t_go_mem 124 x 7
output_single_id_txt:739|MetaEngine> Passed: 0.0 secs, GO Enrichment
output_single_id_txt:739|MetaEngine::analysis> Passed: 6.0 secs, ***** QC ANALYSIS
output_single_id_txt:739|MetaEngine::analysis> Passed: 0.0 secs, ****** PLOT CIRCOS
output_single_id_txt:739|MetaEngine> Passed: 4.0 secs, Start Plot GO
output_single_id_txt:739|WARN> Cannot connect to Cytoscape server!
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 174, in _new_conn
conn = connection.create_connection(
File "/usr/local/lib/python3.9/site-packages/urllib3/util/connection.py", line 95, in create_connection
raise err
File "/usr/local/lib/python3.9/site-packages/urllib3/util/connection.py", line 85, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 703, in urlopen
httplib_response = self._make_request(
File "/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 398, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 239, in request
super(HTTPConnection, self).request(method, url, body=body, headers=headers)
File "/usr/local/lib/python3.9/http/client.py", line 1279, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/local/lib/python3.9/http/client.py", line 1325, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.9/http/client.py", line 1274, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.9/http/client.py", line 1034, in _send_output
self.send(msg)
File "/usr/local/lib/python3.9/http/client.py", line 974, in send
self.connect()
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 205, in connect
conn = self._new_conn()
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 186, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fae6e2a14c0>: Failed to establish a new connection: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/requests/adapters.py", line 440, in send
resp = conn.urlopen(
File "/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 785, in urlopen
retries = retries.increment(
File "/usr/local/lib/python3.9/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='localhost', port=1234): Max retries exceeded with url: /v1/styles/visualproperties (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fae6e2a14c0>: Failed to establish a new connection: [Errno 111] Connection refused'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/meta_test/mylib/ms/biolists.py", line 1331, in __init__
self.cc=cyto.CytoscapeClient(host=host, port=port)
File "/home/meta_test/mylib/cytoscape.py", line 61, in __init__
self.cy = CyRestClient(ip=self.host, port=self.port, version=self.version)
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/cyrest_client.py", line 19, in __init__
self.style = StyleClient(self.__url)
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/style_client.py", line 16, in __init__
self.vps = VisualProperties(url)
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/style_client.py", line 77, in __init__
self.__convert_to_dict()
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/style_client.py", line 80, in __convert_to_dict
vps = requests.get(self.__url).json()
File "/usr/local/lib/python3.9/site-packages/requests/api.py", line 75, in get
return request('get', url, params=params, **kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/api.py", line 61, in request
return session.request(method=method, url=url, **kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/sessions.py", line 529, in request
resp = self.send(prep, **send_kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/sessions.py", line 645, in send
r = adapter.send(request, **kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/adapters.py", line 519, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=1234): Max retries exceeded with url: /v1/styles/visualproperties (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fae6e2a14c0>: Failed to establish a new connection: [Errno 111] Connection refused'))
output_single_id_txt:739|WARN> error during plot_go_network(): /data/output_single_id_txt/Enrichment_GO/GONetwork.xgmml
<class 'AttributeError'>
Traceback (most recent call last):
File "/home/meta_test/mylib/ms/biolists.py", line 1590, in plot_go_network
self.cc.gc()
AttributeError: 'NoneType' object has no attribute 'gc'
Save session file: /data/output_single_id_txt/Enrichment_GO/GONetwork.cys
output_single_id_txt:739|MetaEngine> Passed: 0.0 secs, CytoPlot
output_single_id_txt:739|MetaEngine::analysis> Passed: 0.0 secs, **** PLOT GO
output_single_id_txt:739|WARN> Cannot connect to Cytoscape server!
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 174, in _new_conn
conn = connection.create_connection(
File "/usr/local/lib/python3.9/site-packages/urllib3/util/connection.py", line 95, in create_connection
raise err
File "/usr/local/lib/python3.9/site-packages/urllib3/util/connection.py", line 85, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 703, in urlopen
httplib_response = self._make_request(
File "/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 398, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 239, in request
super(HTTPConnection, self).request(method, url, body=body, headers=headers)
File "/usr/local/lib/python3.9/http/client.py", line 1279, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/local/lib/python3.9/http/client.py", line 1325, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.9/http/client.py", line 1274, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.9/http/client.py", line 1034, in _send_output
self.send(msg)
File "/usr/local/lib/python3.9/http/client.py", line 974, in send
self.connect()
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 205, in connect
conn = self._new_conn()
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 186, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fae98acc7c0>: Failed to establish a new connection: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/requests/adapters.py", line 440, in send
resp = conn.urlopen(
File "/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 785, in urlopen
retries = retries.increment(
File "/usr/local/lib/python3.9/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='localhost', port=1234): Max retries exceeded with url: /v1/styles/visualproperties (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fae98acc7c0>: Failed to establish a new connection: [Errno 111] Connection refused'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/meta_test/mylib/ms/biolists.py", line 1331, in __init__
self.cc=cyto.CytoscapeClient(host=host, port=port)
File "/home/meta_test/mylib/cytoscape.py", line 61, in __init__
self.cy = CyRestClient(ip=self.host, port=self.port, version=self.version)
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/cyrest_client.py", line 19, in __init__
self.style = StyleClient(self.__url)
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/style_client.py", line 16, in __init__
self.vps = VisualProperties(url)
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/style_client.py", line 77, in __init__
self.__convert_to_dict()
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/style_client.py", line 80, in __convert_to_dict
vps = requests.get(self.__url).json()
File "/usr/local/lib/python3.9/site-packages/requests/api.py", line 75, in get
return request('get', url, params=params, **kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/api.py", line 61, in request
return session.request(method=method, url=url, **kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/sessions.py", line 529, in request
resp = self.send(prep, **send_kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/sessions.py", line 645, in send
r = adapter.send(request, **kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/adapters.py", line 519, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=1234): Max retries exceeded with url: /v1/styles/visualproperties (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fae98acc7c0>: Failed to establish a new connection: [Errno 111] Connection refused'))
output_single_id_txt:739|MetaEngine> Passed: 0.0 secs, Start Plot PPI
output_single_id_txt:739|WARN> Error during plot_ppi_network(): /data/output_single_id_txt/Enrichment_PPI/xgmml/Gene_MCODE_ALL.xgmml
/data/output_single_id_txt/Enrichment_PPI/xgmml/Gene.xgmml
<class 'AttributeError'>
Traceback (most recent call last):
File "/home/meta_test/mylib/ms/biolists.py", line 1602, in plot_ppi_network
self.cc.gc()
AttributeError: 'NoneType' object has no attribute 'gc'
output_single_id_txt:739|MetaEngine> Passed: 0.0 secs, Plot PPI
output_single_id_txt:739|MetaEngine::analysis> Passed: 0.0 secs, ***** PLOT PPI
COMPLETE> job #1, input=/data/example/single_list_id.txt, output=/data/output_single_id_txt
output_single_id_txt:739|WARN> Cannot connect to Cytoscape server!
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 174, in _new_conn
conn = connection.create_connection(
File "/usr/local/lib/python3.9/site-packages/urllib3/util/connection.py", line 95, in create_connection
raise err
File "/usr/local/lib/python3.9/site-packages/urllib3/util/connection.py", line 85, in create_connection
sock.connect(sa)
ConnectionRefusedError: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 703, in urlopen
httplib_response = self._make_request(
File "/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 398, in _make_request
conn.request(method, url, **httplib_request_kw)
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 239, in request
super(HTTPConnection, self).request(method, url, body=body, headers=headers)
File "/usr/local/lib/python3.9/http/client.py", line 1279, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/local/lib/python3.9/http/client.py", line 1325, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.9/http/client.py", line 1274, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.9/http/client.py", line 1034, in _send_output
self.send(msg)
File "/usr/local/lib/python3.9/http/client.py", line 974, in send
self.connect()
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 205, in connect
conn = self._new_conn()
File "/usr/local/lib/python3.9/site-packages/urllib3/connection.py", line 186, in _new_conn
raise NewConnectionError(
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection object at 0x7fae712ea760>: Failed to establish a new connection: [Errno 111] Connection refused
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.9/site-packages/requests/adapters.py", line 440, in send
resp = conn.urlopen(
File "/usr/local/lib/python3.9/site-packages/urllib3/connectionpool.py", line 785, in urlopen
retries = retries.increment(
File "/usr/local/lib/python3.9/site-packages/urllib3/util/retry.py", line 592, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPConnectionPool(host='localhost', port=1234): Max retries exceeded with url: /v1/styles/visualproperties (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fae712ea760>: Failed to establish a new connection: [Errno 111] Connection refused'))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/meta_test/mylib/ms/biolists.py", line 1331, in __init__
self.cc=cyto.CytoscapeClient(host=host, port=port)
File "/home/meta_test/mylib/cytoscape.py", line 61, in __init__
self.cy = CyRestClient(ip=self.host, port=self.port, version=self.version)
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/cyrest_client.py", line 19, in __init__
self.style = StyleClient(self.__url)
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/style_client.py", line 16, in __init__
self.vps = VisualProperties(url)
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/style_client.py", line 77, in __init__
self.__convert_to_dict()
File "/usr/local/lib/python3.9/site-packages/py2cytoscape/data/style_client.py", line 80, in __convert_to_dict
vps = requests.get(self.__url).json()
File "/usr/local/lib/python3.9/site-packages/requests/api.py", line 75, in get
return request('get', url, params=params, **kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/api.py", line 61, in request
return session.request(method=method, url=url, **kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/sessions.py", line 529, in request
resp = self.send(prep, **send_kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/sessions.py", line 645, in send
r = adapter.send(request, **kwargs)
File "/usr/local/lib/python3.9/site-packages/requests/adapters.py", line 519, in send
raise ConnectionError(e, request=request)
requests.exceptions.ConnectionError: HTTPConnectionPool(host='localhost', port=1234): Max retries exceeded with url: /v1/styles/visualproperties (Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at 0x7fae712ea760>: Failed to establish a new connection: [Errno 111] Connection refused'))`