Hello, thanks for sharing the package. It is very interesting work.
But when I just submit the job using the example data you provided in cluster, I have errors as below:
Loaded Nothing - invalid DIR structure:
/tsl/software/testing/bin/core/../..//meme/5.1.1/
Loaded Nothing - invalid DIR structure:
/tsl/software/production/bin/core/../..//hpccore/5/
Loaded Nothing - invalid DIR structure:
/tsl/software/testing/bin/core/../..//conda/3.7/
2022-04-28 17:58:34 INFO checking MEME...
2022-04-28 17:58:34 INFO Input matrix has # rows: 428, # columns: 5
2022-04-28 17:58:34 INFO # clusters/row: 2
2022-04-28 17:58:34 INFO # clusters/column: 29
2022-04-28 17:58:34 INFO # CLUSTERS: 43
2022-04-28 17:58:34 INFO use operons: 1
2022-04-28 17:58:34 INFO using MEME version 4.9.0
/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py:109: SAWarning: relationship 'MotifPSSMRow.motif_info' will copy column motif_infos.rowid to column motif_pssm_rows.motif_info_id, which conflicts with relationship(s): 'MotifInfo.pssm_rows' (copies motif_infos.rowid to motif_pssm_rows.motif_info_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="pssm_rows"' to the 'MotifPSSMRow.motif_info' relationship. (Background on this error at: https://sqlalche.me/e/14/qzyx)
for index in xrange(len(self.ratios.row_names))]
/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py:109: SAWarning: relationship 'MemeMotifSite.motif_info' will copy column motif_infos.rowid to column meme_motif_sites.motif_info_id, which conflicts with relationship(s): 'MotifInfo.sites' (copies motif_infos.rowid to meme_motif_sites.motif_info_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="sites"' to the 'MemeMotifSite.motif_info' relationship. (Background on this error at: https://sqlalche.me/e/14/qzyx)
for index in xrange(len(self.ratios.row_names))]
/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py:109: SAWarning: relationship 'MotifAnnotation.motif_info' will copy column motif_infos.rowid to column motif_annotations.motif_info_id, which conflicts with relationship(s): 'MotifInfo.annotations' (copies motif_infos.rowid to motif_annotations.motif_info_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="annotations"' to the 'MotifAnnotation.motif_info' relationship. (Background on this error at: https://sqlalche.me/e/14/qzyx)
for index in xrange(len(self.ratios.row_names))]
2022-04-28 17:58:35 INFO attempting automatic download of operons from Microbes Online
2022-04-28 17:58:35 INFO Loading STRING file at '64091'
Traceback (most recent call last):
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 1319, in do_open
encode_chunked=req.has_header('Transfer-encoding'))
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 1252, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 1298, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 1247, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 1026, in _send_output
self.send(msg)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 966, in send
self.connect()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/socket.py", line 728, in create_connection
raise err
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/socket.py", line 716, in create_connection
sock.connect(sa)
TimeoutError: [Errno 110] Connection timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/tsl/software/testing/bin/core/../..//conda/3.7/x86_64/bin/cmonkey2", line 37, in
cmonkey_run.run()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py", line 441, in run
self.prepare_run()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py", line 407, in prepare_run
thesaurus = self.organism().thesaurus()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py", line 156, in organism
self.organism = self.make_organism()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py", line 255, in make_organism
ncbi_code)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/organism.py", line 34, in init__
self.species = rsatdb.get_rsat_organism(kegg_organism)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/rsat.py", line 104, in get_rsat_organism
cache_file).decode('utf-8')
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/util.py", line 255, in read_url_cached
outfile.write(read_url(url))
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/util.py", line 244, in read_url
return urlopen(url).read()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 110] Connection timed out>
Do you think it is because of improper installation? or some other problems?
Hello, thanks for sharing the package. It is very interesting work. But when I just submit the job using the example data you provided in cluster, I have errors as below:
Loaded Nothing - invalid DIR structure: /tsl/software/testing/bin/core/../..//meme/5.1.1/ Loaded Nothing - invalid DIR structure: /tsl/software/production/bin/core/../..//hpccore/5/ Loaded Nothing - invalid DIR structure: /tsl/software/testing/bin/core/../..//conda/3.7/ 2022-04-28 17:58:34 INFO checking MEME... 2022-04-28 17:58:34 INFO Input matrix has # rows: 428, # columns: 5 2022-04-28 17:58:34 INFO # clusters/row: 2 2022-04-28 17:58:34 INFO # clusters/column: 29 2022-04-28 17:58:34 INFO # CLUSTERS: 43 2022-04-28 17:58:34 INFO use operons: 1 2022-04-28 17:58:34 INFO using MEME version 4.9.0 /tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py:109: SAWarning: relationship 'MotifPSSMRow.motif_info' will copy column motif_infos.rowid to column motif_pssm_rows.motif_info_id, which conflicts with relationship(s): 'MotifInfo.pssm_rows' (copies motif_infos.rowid to motif_pssm_rows.motif_info_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="pssm_rows"' to the 'MotifPSSMRow.motif_info' relationship. (Background on this error at: https://sqlalche.me/e/14/qzyx) for index in xrange(len(self.ratios.row_names))] /tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py:109: SAWarning: relationship 'MemeMotifSite.motif_info' will copy column motif_infos.rowid to column meme_motif_sites.motif_info_id, which conflicts with relationship(s): 'MotifInfo.sites' (copies motif_infos.rowid to meme_motif_sites.motif_info_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="sites"' to the 'MemeMotifSite.motif_info' relationship. (Background on this error at: https://sqlalche.me/e/14/qzyx) for index in xrange(len(self.ratios.row_names))] /tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py:109: SAWarning: relationship 'MotifAnnotation.motif_info' will copy column motif_infos.rowid to column motif_annotations.motif_info_id, which conflicts with relationship(s): 'MotifInfo.annotations' (copies motif_infos.rowid to motif_annotations.motif_info_id). If this is not the intention, consider if these relationships should be linked with back_populates, or if viewonly=True should be applied to one or more if they are read-only. For the less common case that foreign key constraints are partially overlapping, the orm.foreign() annotation can be used to isolate the columns that should be written towards. To silence this warning, add the parameter 'overlaps="annotations"' to the 'MotifAnnotation.motif_info' relationship. (Background on this error at: https://sqlalche.me/e/14/qzyx) for index in xrange(len(self.ratios.row_names))] 2022-04-28 17:58:35 INFO attempting automatic download of operons from Microbes Online 2022-04-28 17:58:35 INFO Loading STRING file at '64091' Traceback (most recent call last): File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 1319, in do_open encode_chunked=req.has_header('Transfer-encoding')) File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 1252, in request self._send_request(method, url, body, headers, encode_chunked) File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 1298, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 1247, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 1026, in _send_output self.send(msg) File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 966, in send self.connect() File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/http/client.py", line 938, in connect (self.host,self.port), self.timeout, self.source_address) File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/socket.py", line 728, in create_connection raise err File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/socket.py", line 716, in create_connection sock.connect(sa) TimeoutError: [Errno 110] Connection timed out
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/tsl/software/testing/bin/core/../..//conda/3.7/x86_64/bin/cmonkey2", line 37, in
cmonkey_run.run()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py", line 441, in run
self.prepare_run()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py", line 407, in prepare_run
thesaurus = self.organism().thesaurus()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py", line 156, in organism
self.organism = self.make_organism()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/cmonkey_run.py", line 255, in make_organism
ncbi_code)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/organism.py", line 34, in init__
self.species = rsatdb.get_rsat_organism(kegg_organism)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/rsat.py", line 104, in get_rsat_organism
cache_file).decode('utf-8')
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/util.py", line 255, in read_url_cached
outfile.write(read_url(url))
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/site-packages/cmonkey/util.py", line 244, in read_url
return urlopen(url).read()
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 525, in open
response = self._open(req, data)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 543, in _open
'_open', req)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 1347, in http_open
return self.do_open(http.client.HTTPConnection, req)
File "/tsl/software/testing/conda/3.7/x86_64/lib/python3.7/urllib/request.py", line 1321, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno 110] Connection timed out>
Do you think it is because of improper installation? or some other problems?
Thank you so much.