how to use evcouplings

[yzcha0]

Hi! I try to use evcouplings for MSA, but an error occurred.

Traceback (most recent call last): File "/home/zcyan/miniconda3/lib/python3.10/urllib/request.py", line 1565, in ftp_open fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout) File "/home/zcyan/miniconda3/lib/python3.10/urllib/request.py", line 1585, in connect_ftp return ftpwrapper(user, passwd, host, port, dirs, timeout, File "/home/zcyan/miniconda3/lib/python3.10/urllib/request.py", line 2406, in init self.init() File "/home/zcyan/miniconda3/lib/python3.10/urllib/request.py", line 2416, in init self.ftp.login(self.user, self.passwd) File "/home/zcyan/miniconda3/lib/python3.10/ftplib.py", line 412, in login resp = self.sendcmd('USER ' + user) File "/home/zcyan/miniconda3/lib/python3.10/ftplib.py", line 281, in sendcmd return self.getresp() File "/home/zcyan/miniconda3/lib/python3.10/ftplib.py", line 244, in getresp resp = self.getmultiline() File "/home/zcyan/miniconda3/lib/python3.10/ftplib.py", line 230, in getmultiline line = self.getline() File "/home/zcyan/miniconda3/lib/python3.10/ftplib.py", line 212, in getline line = self.file.readline(self.maxline + 1) File "/home/zcyan/miniconda3/lib/python3.10/socket.py", line 705, in readinto return self._sock.recv_into(b) ConnectionResetError: [Errno 104] Connection reset by peer

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/zcyan/miniconda3/lib/python3.10/site-packages/evcouplings/utils/pipeline.py", line 508, in execute_wrapped outcfg = execute(config) File "/home/zcyan/miniconda3/lib/python3.10/site-packages/evcouplings/utils/pipeline.py", line 187, in execute outcfg = runner(incfg) File "/home/zcyan/miniconda3/lib/python3.10/site-packages/evcouplings/compare/protocol.py", line 1250, in run return PROTOCOLSkwargs["protocol"] File "/home/zcyan/miniconda3/lib/python3.10/site-packages/evcouplings/compare/protocol.py", line 653, in standard sifts_map, sifts_map_full = _identify_structures(*{ File "/home/zcyan/miniconda3/lib/python3.10/site-packages/evcouplings/compare/protocol.py", line 152, in _identify_structures s = SIFTS( File "/home/zcyan/miniconda3/lib/python3.10/site-packages/evcouplings/compare/sifts.py", line 339, in init self._create_mapping_table(sifts_table_file) File "/home/zcyan/miniconda3/lib/python3.10/site-packages/evcouplings/compare/sifts.py", line 405, in _create_mapping_table get_urllib(SIFTS_URL, temp_download_file) File "/home/zcyan/miniconda3/lib/python3.10/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/zcyan/miniconda3/lib/python3.10/urllib/request.py", line 216, in urlopen return opener.open(url, data, timeout) File "/home/zcyan/miniconda3/lib/python3.10/urllib/request.py", line 519, in open response = self._open(req, data) File "/home/zcyan/miniconda3/lib/python3.10/urllib/request.py", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + File "/home/zcyan/miniconda3/lib/python3.10/urllib/request.py", line 496, in _call_chain result = func(args) File "/home/zcyan/miniconda3/lib/python3.10/urllib/request.py", line 1582, in ftp_open raise URLError(exp) from exp

[yzcha0]

Hi, You can see the script here plz: https://github.com/tyang816/ProtREM?tab=readme-ov-file#search-homology-sequences-by-jackhmmer

I run the step 1 And I have set up the PLMC path in the config file, single_comfig_manomer.txt. Do I need to make any other modifications in this file?

[tyang816]

Actually no, hh, I have never met this problem...

[tyang816]

Is the network on your server normal? It looks like a request error.

[yzcha0]

Is the network on your server normal? It looks like a request error. yes, it's a request error. orz