Error happened using WHISCY

HADDOCK
1

Dear all,
Hi, I’m trying to run protein-protein docking using HADDOCK 2.4 webserver, and I have to find the active residues when I set up this docking. Thus, I currently use the WHISCHY to predict one of two protein’s active residues but the following errors always happen: # Could you help me fix this issue? Thank you so much .

===========================================================================
command: whiscy_setup ClfA_1N67_229-560_PreprocessedbyMaestro.pdb C
exit status: 1
log:
2024-06-23 17:01:08,238 cli_setup:192 INFO - PDB structure with chain C saved to ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
2024-06-23 17:01:08,295 cli_setup:199 INFO - Atom accessibility calculated to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rsa
2024-06-23 17:01:08,296 cli_setup:203 INFO - Surface and buried residues calculated
2024-06-23 17:01:08,325 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-06-23 17:01:08,325 cli_setup:253 INFO - Running blastp via NCBI
Traceback (most recent call last):
File "/usr/local/lib/python3.11/urllib/request.py", line 1348, in do_open
h.request(req.get_method(), req.selector, req.data, headers,
File "/usr/local/lib/python3.11/http/client.py", line 1303, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/usr/local/lib/python3.11/http/client.py", line 1349, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.11/http/client.py", line 1298, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/usr/local/lib/python3.11/http/client.py", line 1058, in _send_output
self.send(msg)
File "/usr/local/lib/python3.11/http/client.py", line 996, in send
self.connect()
File "/usr/local/lib/python3.11/http/client.py", line 1468, in connect
super().connect()
File "/usr/local/lib/python3.11/http/client.py", line 962, in connect
self.sock = self._create_connection(
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/socket.py", line 827, in create_connection
for res in getaddrinfo(host, port, 0, SOCK_STREAM):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/socket.py", line 962, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
socket.gaierror: [Errno -3] Temporary failure in name resolution

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/usr/local/bin/whiscy_setup", line 6, in <module>
sys.exit(main())
^^^^^^
File "/opt/software/whiscy/src/whiscy/cli_setup.py", line 254, in main
ncbi_blast(input_sequence_file, blast_output_file)
File "/opt/software/whiscy/src/whiscy/cli_setup.py", line 63, in ncbi_blast
result_handle = NCBIWWW.qblast("blastp", "nr", record.format("fasta"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/Bio/Blast/NCBIWWW.py", line 204, in qblast
handle = urlopen(request)
^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/urllib/request.py", line 216, in urlopen
return opener.open(url, data, timeout)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/urllib/request.py", line 519, in open
response = self._open(req, data)
^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/urllib/request.py", line 536, in _open
result = self._call_chain(self.handle_open, protocol, protocol +
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/urllib/request.py", line 496, in _call_chain
result = func(*args)
^^^^^^^^^^^
File "/usr/local/lib/python3.11/urllib/request.py", line 1391, in https_open
return self.do_open(http.client.HTTPSConnection, req,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/urllib/request.py", line 1351, in do_open
raise URLError(err)
urllib.error.URLError: <urlopen error [Errno -3] Temporary failure in name resolution>
2

Dear Jasen,

Looking at the error, it seems like it came from the NCBI blasp call.
This may be caused because of some issues on their side while using the api.

Please retry it a little bit later, hoping that they will fix their problem.
By the time, we will also check the code on our side.

Best regards

3

Hi @7dGss, thanks for reporting this issue.

There was a small glitch in the configuration of Whiscy which has now been patched, please try to re-submit your job.

4

Hi,
I tried it again but the following errors happen whatever I use original PDB file downloaded from PDB bank or the pre-processed PDB by Schrodinger software. Could you help me?

#===========================================================================
command: whiscy_setup ClfA_1N67_229-560_PreprocessedbyMaestro.pdb C
exit status: 0
log:
2024-06-24 16:18:37,541 cli_setup:192 INFO - PDB structure with chain C saved to ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
2024-06-24 16:18:37,597 cli_setup:199 INFO - Atom accessibility calculated to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rsa
2024-06-24 16:18:37,598 cli_setup:203 INFO - Surface and buried residues calculated
2024-06-24 16:18:37,627 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-06-24 16:18:37,627 cli_setup:253 INFO - Running blastp via NCBI
2024-06-24 16:29:39,993 cli_setup:255 INFO - Result stored in ClfA_1N67_229-560_PreprocessedbyMaestro_C_blast.xml
2024-06-24 16:29:40,002 cli_setup:268 INFO - Generating MSA using MUSCLE...
2024-06-24 16:29:40,174 cli_setup:271 INFO - Done.
2024-06-24 16:29:40,175 cli_setup:274 INFO - Converting MSA file to Phylseq format...
2024-06-24 16:29:40,175 cli_setup:283 INFO - ClfA_1N67_229-560_PreprocessedbyMaestro_C.phylseq file written
2024-06-24 16:29:40,177 cli_setup:310 INFO - Protdist calculated
2024-06-24 16:29:40,206 cli_setup:317 INFO - Conversion table file generated
2024-06-24 16:29:40,206 cli_setup:319 INFO - Whiscy setup finished
command: whiscy ClfA_1N67_229-560_PreprocessedbyMaestro_C.sur ClfA_1N67_229-560_PreprocessedbyMaestro_C.conv ClfA_1N67_229-560_PreprocessedbyMaestro_C.phylseq ClfA_1N67_229-560_PreprocessedbyMaestro_C.out -o ClfA_1N67_229-560_PreprocessedbyMaestro_C.cons
exit status: 0
log:
2024-06-24 16:18:37,541 cli_setup:192 INFO - PDB structure with chain C saved to ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
2024-06-24 16:18:37,597 cli_setup:199 INFO - Atom accessibility calculated to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rsa
2024-06-24 16:18:37,598 cli_setup:203 INFO - Surface and buried residues calculated
2024-06-24 16:18:37,627 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-06-24 16:18:37,627 cli_setup:253 INFO - Running blastp via NCBI
2024-06-24 16:29:39,993 cli_setup:255 INFO - Result stored in ClfA_1N67_229-560_PreprocessedbyMaestro_C_blast.xml
2024-06-24 16:29:40,002 cli_setup:268 INFO - Generating MSA using MUSCLE...
2024-06-24 16:29:40,174 cli_setup:271 INFO - Done.
2024-06-24 16:29:40,175 cli_setup:274 INFO - Converting MSA file to Phylseq format...
2024-06-24 16:29:40,175 cli_setup:283 INFO - ClfA_1N67_229-560_PreprocessedbyMaestro_C.phylseq file written
2024-06-24 16:29:40,177 cli_setup:310 INFO - Protdist calculated
2024-06-24 16:29:40,206 cli_setup:317 INFO - Conversion table file generated
2024-06-24 16:29:40,206 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
command: whiscy ClfA_1N67_229-560_PreprocessedbyMaestro_C.lac ClfA_1N67_229-560_PreprocessedbyMaestro_C.conv ClfA_1N67_229-560_PreprocessedbyMaestro_C.phylseq ClfA_1N67_229-560_PreprocessedbyMaestro_C.out -o ClfA_1N67_229-560_PreprocessedbyMaestro_C.lcons
exit status: 0
log:
2024-06-24 16:18:37,541 cli_setup:192 INFO - PDB structure with chain C saved to ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
2024-06-24 16:18:37,597 cli_setup:199 INFO - Atom accessibility calculated to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rsa
2024-06-24 16:18:37,598 cli_setup:203 INFO - Surface and buried residues calculated
2024-06-24 16:18:37,627 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-06-24 16:18:37,627 cli_setup:253 INFO - Running blastp via NCBI
2024-06-24 16:29:39,993 cli_setup:255 INFO - Result stored in ClfA_1N67_229-560_PreprocessedbyMaestro_C_blast.xml
2024-06-24 16:29:40,002 cli_setup:268 INFO - Generating MSA using MUSCLE...
2024-06-24 16:29:40,174 cli_setup:271 INFO - Done.
2024-06-24 16:29:40,175 cli_setup:274 INFO - Converting MSA file to Phylseq format...
2024-06-24 16:29:40,175 cli_setup:283 INFO - ClfA_1N67_229-560_PreprocessedbyMaestro_C.phylseq file written
2024-06-24 16:29:40,177 cli_setup:310 INFO - Protdist calculated
2024-06-24 16:29:40,206 cli_setup:317 INFO - Conversion table file generated
2024-06-24 16:29:40,206 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
command: whiscy_consadjust ClfA_1N67_229-560_PreprocessedbyMaestro_C.cons -o ClfA_1N67_229-560_PreprocessedbyMaestro_C.acons
exit status: 0
log:
2024-06-24 16:18:37,541 cli_setup:192 INFO - PDB structure with chain C saved to ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
2024-06-24 16:18:37,597 cli_setup:199 INFO - Atom accessibility calculated to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rsa
2024-06-24 16:18:37,598 cli_setup:203 INFO - Surface and buried residues calculated
2024-06-24 16:18:37,627 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-06-24 16:18:37,627 cli_setup:253 INFO - Running blastp via NCBI
2024-06-24 16:29:39,993 cli_setup:255 INFO - Result stored in ClfA_1N67_229-560_PreprocessedbyMaestro_C_blast.xml
2024-06-24 16:29:40,002 cli_setup:268 INFO - Generating MSA using MUSCLE...
2024-06-24 16:29:40,174 cli_setup:271 INFO - Done.
2024-06-24 16:29:40,175 cli_setup:274 INFO - Converting MSA file to Phylseq format...
2024-06-24 16:29:40,175 cli_setup:283 INFO - ClfA_1N67_229-560_PreprocessedbyMaestro_C.phylseq file written
2024-06-24 16:29:40,177 cli_setup:310 INFO - Protdist calculated
2024-06-24 16:29:40,206 cli_setup:317 INFO - Conversion table file generated
2024-06-24 16:29:40,206 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file ClfA_1N67_229-560_PreprocessedbyMaestro_C.cons does not exist
command: whiscy_resdist ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb ClfA_1N67_229-560_PreprocessedbyMaestro_C.conv ClfA_1N67_229-560_PreprocessedbyMaestro_C.rd
exit status: 0
log:
2024-06-24 16:18:37,541 cli_setup:192 INFO - PDB structure with chain C saved to ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
2024-06-24 16:18:37,597 cli_setup:199 INFO - Atom accessibility calculated to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rsa
2024-06-24 16:18:37,598 cli_setup:203 INFO - Surface and buried residues calculated
2024-06-24 16:18:37,627 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-06-24 16:18:37,627 cli_setup:253 INFO - Running blastp via NCBI
2024-06-24 16:29:39,993 cli_setup:255 INFO - Result stored in ClfA_1N67_229-560_PreprocessedbyMaestro_C_blast.xml
2024-06-24 16:29:40,002 cli_setup:268 INFO - Generating MSA using MUSCLE...
2024-06-24 16:29:40,174 cli_setup:271 INFO - Done.
2024-06-24 16:29:40,175 cli_setup:274 INFO - Converting MSA file to Phylseq format...
2024-06-24 16:29:40,175 cli_setup:283 INFO - ClfA_1N67_229-560_PreprocessedbyMaestro_C.phylseq file written
2024-06-24 16:29:40,177 cli_setup:310 INFO - Protdist calculated
2024-06-24 16:29:40,206 cli_setup:317 INFO - Conversion table file generated
2024-06-24 16:29:40,206 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file ClfA_1N67_229-560_PreprocessedbyMaestro_C.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
residue_distance [INFO] Residue distances written to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rd
command: whiscy_parasmooth ClfA_1N67_229-560_PreprocessedbyMaestro_C.acons ClfA_1N67_229-560_PreprocessedbyMaestro_C.lcons ClfA_1N67_229-560_PreprocessedbyMaestro_C.rd -o ClfA_1N67_229-560_PreprocessedbyMaestro_C.pscons
exit status: 0
log:
2024-06-24 16:18:37,541 cli_setup:192 INFO - PDB structure with chain C saved to ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
2024-06-24 16:18:37,597 cli_setup:199 INFO - Atom accessibility calculated to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rsa
2024-06-24 16:18:37,598 cli_setup:203 INFO - Surface and buried residues calculated
2024-06-24 16:18:37,627 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-06-24 16:18:37,627 cli_setup:253 INFO - Running blastp via NCBI
2024-06-24 16:29:39,993 cli_setup:255 INFO - Result stored in ClfA_1N67_229-560_PreprocessedbyMaestro_C_blast.xml
2024-06-24 16:29:40,002 cli_setup:268 INFO - Generating MSA using MUSCLE...
2024-06-24 16:29:40,174 cli_setup:271 INFO - Done.
2024-06-24 16:29:40,175 cli_setup:274 INFO - Converting MSA file to Phylseq format...
2024-06-24 16:29:40,175 cli_setup:283 INFO - ClfA_1N67_229-560_PreprocessedbyMaestro_C.phylseq file written
2024-06-24 16:29:40,177 cli_setup:310 INFO - Protdist calculated
2024-06-24 16:29:40,206 cli_setup:317 INFO - Conversion table file generated
2024-06-24 16:29:40,206 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file ClfA_1N67_229-560_PreprocessedbyMaestro_C.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
residue_distance [INFO] Residue distances written to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: 'ClfA_1N67_229-560_PreprocessedbyMaestro_C.acons'
command: whiscy_bfactor ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb ClfA_1N67_229-560_PreprocessedbyMaestro_C_bfactor.pdb ClfA_1N67_229-560_PreprocessedbyMaestro_C.pscons
exit status: 1
log:
2024-06-24 16:18:37,541 cli_setup:192 INFO - PDB structure with chain C saved to ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
2024-06-24 16:18:37,597 cli_setup:199 INFO - Atom accessibility calculated to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rsa
2024-06-24 16:18:37,598 cli_setup:203 INFO - Surface and buried residues calculated
2024-06-24 16:18:37,627 cli_setup:246 INFO - HSSP file not found, fallback to generating MSA with blastp
2024-06-24 16:18:37,627 cli_setup:253 INFO - Running blastp via NCBI
2024-06-24 16:29:39,993 cli_setup:255 INFO - Result stored in ClfA_1N67_229-560_PreprocessedbyMaestro_C_blast.xml
2024-06-24 16:29:40,002 cli_setup:268 INFO - Generating MSA using MUSCLE...
2024-06-24 16:29:40,174 cli_setup:271 INFO - Done.
2024-06-24 16:29:40,175 cli_setup:274 INFO - Converting MSA file to Phylseq format...
2024-06-24 16:29:40,175 cli_setup:283 INFO - ClfA_1N67_229-560_PreprocessedbyMaestro_C.phylseq file written
2024-06-24 16:29:40,177 cli_setup:310 INFO - Protdist calculated
2024-06-24 16:29:40,206 cli_setup:317 INFO - Conversion table file generated
2024-06-24 16:29:40,206 cli_setup:319 INFO - Whiscy setup finished
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
whiscy [INFO] Parsing surface list...
whiscy [INFO] Loading conversion table...
whiscy [INFO] Converting...
whiscy [INFO] Initializing score calculation...
whiscy [ERROR] Can not read sequence number
consadjust [ERROR] Conservation file ClfA_1N67_229-560_PreprocessedbyMaestro_C.cons does not exist
residue_distance [INFO] Reading conversion table
residue_distance [INFO] Reading PDB structure from ClfA_1N67_229-560_PreprocessedbyMaestro_C.pdb
residue_distance [INFO] Residue distances written to ClfA_1N67_229-560_PreprocessedbyMaestro_C.rd
parasmooth [INFO] Reading input files
parasmooth [ERROR] [Errno 2] No such file or directory: 'ClfA_1N67_229-560_PreprocessedbyMaestro_C.acons'
Traceback (most recent call last):
File "/usr/local/bin/whiscy_bfactor", line 6, in <module>
sys.exit(main())
^^^^^^
File "/opt/software/whiscy/src/whiscy/cli_bfactor.py", line 68, in main
scores = parse_whiscy_scores(whiscy_scores_file_name)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/software/whiscy/src/whiscy/cli_bfactor.py", line 31, in parse_whiscy_scores
with open(file_name) as input:
^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'ClfA_1N67_229-560_PreprocessedbyMaestro_C.pscons'
5

Thanks for your kind attention. I encountered another error like the above.

6

Thank you for the follow up @7dGss, this log is quite informative. I can see that there are unfortunately a few things wrong with the source code (this is unrelated to the web service at this point). The exit signals are wrong, which then causes a cascade of errors. I will address these in the code (Issues · haddocking/whiscy · GitHub)

However for your specific case it seems that Whiscy cannot read the alignment that it produced, which is very weird. If possible, could you please send the input structure to bonvinlab.support@uu.nl? That will make debuging it much easier.