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debbiemarkslab / EVcouplings

Evolutionary couplings from protein and RNA sequence alignments
http://evcouplings.org
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Error at compare stage of EV couplings complex: Unable to download and acess files from SIFT database #290

Closed sudhabioinfo87 closed 1 year ago

sudhabioinfo87 commented 1 year ago

The configuration file runs till the coupling stage of the workflow. I guess there is a problem in downloading the SIFTS files. Pls find below the error message: /home/sudha/anaconda3/lib/python3.7/site-packages/sklearn/utils/validation.py:37: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. LARGE_SPARSE_SUPPORTED = LooseVersion(scipy_version) >= '0.14.0' /home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/visualize/parameters.py:137: RuntimeWarning: divide by zero encountered in log2 B = -fi np.log2(fi) /home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/visualize/parameters.py:137: RuntimeWarning: invalid value encountered in multiply B = -fi np.log2(fi) Traceback (most recent call last): File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 1566, in ftp_open fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 1588, in connect_ftp persistent=False) File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 2408, in init self.init() File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 2417, in init self.ftp.connect(self.host, self.port, self.timeout) File "/home/sudha/anaconda3/lib/python3.7/ftplib.py", line 154, in connect source_address=self.source_address) File "/home/sudha/anaconda3/lib/python3.7/socket.py", line 728, in create_connection raise err File "/home/sudha/anaconda3/lib/python3.7/socket.py", line 716, 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 "/home/sudha/anaconda3/bin/evcouplings_runcfg", line 10, in sys.exit(app()) File "/home/sudha/anaconda3/lib/python3.7/site-packages/click/core.py", line 1128, in call return self.main(args, kwargs) File "/home/sudha/anaconda3/lib/python3.7/site-packages/click/core.py", line 1053, in main rv = self.invoke(ctx) File "/home/sudha/anaconda3/lib/python3.7/site-packages/click/core.py", line 1395, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/sudha/anaconda3/lib/python3.7/site-packages/click/core.py", line 754, in invoke return __callback(args, kwargs) File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/utils/pipeline.py", line 583, in app outcfg = run(kwargs) File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/utils/pipeline.py", line 570, in run return execute_wrapped(config) File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/utils/pipeline.py", line 508, in execute_wrapped outcfg = execute(config) File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/utils/pipeline.py", line 187, in execute outcfg = runner(incfg) File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/compare/protocol.py", line 1250, in run return PROTOCOLS[kwargs["protocol"]](kwargs) File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/compare/protocol.py", line 961, in complex outcfg, first_sifts_map = _identify_monomer_structures("first", outcfg, first_aux_prefix) File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/compare/protocol.py", line 947, in _identify_monomer_structures prefix=aux_prefix File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/compare/protocol.py", line 154, in _identify_structures kwargs["sifts_sequence_db"] File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/compare/sifts.py", line 268, in init self._create_mapping_table(sifts_table_file) File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/compare/sifts.py", line 334, in _create_mapping_table get_urllib(SIFTS_URL, temp_download_file) File "/home/sudha/anaconda3/lib/python3.7/site-packages/evcouplings/utils/system.py", line 300, in get_urllib with urllib.request.urlopen(url) as r, open(output_path, 'wb') as f: File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 525, in open response = self._open(req, data) File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 543, in _open '_open', req) File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 503, in _call_chain result = func(*args) File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 1584, in ftp_open raise exc.with_traceback(sys.exc_info()[2]) File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 1566, in ftp_open fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 1588, in connect_ftp persistent=False) File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 2408, in init self.init() File "/home/sudha/anaconda3/lib/python3.7/urllib/request.py", line 2417, in init self.ftp.connect(self.host, self.port, self.timeout) File "/home/sudha/anaconda3/lib/python3.7/ftplib.py", line 154, in connect source_address=self.source_address) File "/home/sudha/anaconda3/lib/python3.7/socket.py", line 728, in create_connection raise err File "/home/sudha/anaconda3/lib/python3.7/socket.py", line 716, in create_connection sock.connect(sa) urllib.error.URLError: <urlopen error ftp error: ConnectionRefusedError(111, 'Connection refused')> Segmentation fault (core dumped)

Pls find attached the config file. Only the path to SIFTS file has been provided. The file map and db are empty filenames. I was hoping that Evcouplings will automatically download the required SIFTS files and paste in the file path I had provided in the config file as follows: sifts_mapping_table: /home/sudha/WORK/programs/evcouplings_support_programs/sifts_map/map sifts_sequence_db: /home/sudha/WORK/programs/evcouplings_support_programs/sifts_seqdb/db

It will be great, if you could please fix this problem. sample_config_complex.txt

thomashopf commented 1 year ago

Can you please try to run this again with the latest version of EVcouplings directly from the develop branch here on github? There have been some fixes recently related to retrieval of sequences for the SIFTS tables.

Additionally, please check your firewall settings, it might be the case that FTP connections are blocked.

thomashopf commented 1 year ago

Assuming as resolved, please reopen if necessary

sudhabioinfo87 commented 1 year ago

Dear EVcouplings team,

Thanks a lot for the reply. Sorry. I could'nt reply earlier. I had to work on other sections of my project. I was racing with time. I was in touch with Daniel Ritter from your group. He had helped me with troubleshooting. I tried out his suggestion .It worked !!! I will try to run batch jobs on the server. I will get in touch if I have problems installing on the server.

Thanks again, Dr. Sudha Govindarajan.

On Wed, May 10, 2023 at 10:03 PM thomashopf @.***> wrote:

Closed #290 https://github.com/debbiemarkslab/EVcouplings/issues/290 as completed.

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