Web services not returning output

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.0.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/lei/Desktop/binder_designing/PD-L1/prototype/38f5286fdff74c2273a65c80f83672790011200005_0000001_08_000000027.pdb

Summary of feedback from opening
/Users/lei/Desktop/binder_designing/PD-L1/prototype/38f5286fdff74c2273a65c80f83672790011200005_0000001_08_000000027.pdb  
---  
warnings | Ignored bad PDB record found on line 2838  
score 0  
  
Ignored bad PDB record found on line 2839  
silent_score 0  
  
Ignored bad PDB record found on line 2840  
  
Chain information for
38f5286fdff74c2273a65c80f83672790011200005_0000001_08_000000027.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lei/Desktop/binder_designing/PD-L1/prototype/AF2_seq/7aa8ad255b67e2a0b85a847565c450fc.pdb

Chain information for 7aa8ad255b67e2a0b85a847565c450fc.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lei/Desktop/binder_designing/PD-L1/prototype/AF2_seq/3182c3916409675a9da448253c103626.pdb

Chain information for 3182c3916409675a9da448253c103626.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lei/Desktop/binder_designing/PD-L1/prototype/AF2_seq/a13c48685cb143163ba0d1073c4ede81.pdb

Chain information for a13c48685cb143163ba0d1073c4ede81.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lei/Desktop/binder_designing/PD-L1/prototype/AF2_seq/b31dcb58a81fd35dcd0b05f2f8a01ac9.pdb

Chain information for b31dcb58a81fd35dcd0b05f2f8a01ac9.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lei/Desktop/binder_designing/PD-L1/prototype/AF2_seq/bb890777c74b6c1dcfe34a96719c20f8.pdb

Chain information for bb890777c74b6c1dcfe34a96719c20f8.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/lei/Desktop/binder_designing/PD-L1/prototype/AF2_seq/c7a4f2905fe45902aa7b512475ab2c7e.pdb

Chain information for c7a4f2905fe45902aa7b512475ab2c7e.pdb #7  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> mmaker #2-7 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker
38f5286fdff74c2273a65c80f83672790011200005_0000001_08_000000027.pdb, chain B
(#1) with 7aa8ad255b67e2a0b85a847565c450fc.pdb, chain B (#2), sequence
alignment score = 536.9  
RMSD between 113 pruned atom pairs is 0.606 angstroms; (across all 114 pairs:
0.928)  
  
Matchmaker
38f5286fdff74c2273a65c80f83672790011200005_0000001_08_000000027.pdb, chain B
(#1) with 3182c3916409675a9da448253c103626.pdb, chain B (#3), sequence
alignment score = 547.7  
RMSD between 113 pruned atom pairs is 0.585 angstroms; (across all 114 pairs:
0.922)  
  
Matchmaker
38f5286fdff74c2273a65c80f83672790011200005_0000001_08_000000027.pdb, chain B
(#1) with a13c48685cb143163ba0d1073c4ede81.pdb, chain B (#4), sequence
alignment score = 536.9  
RMSD between 113 pruned atom pairs is 0.597 angstroms; (across all 114 pairs:
0.924)  
  
Matchmaker
38f5286fdff74c2273a65c80f83672790011200005_0000001_08_000000027.pdb, chain B
(#1) with b31dcb58a81fd35dcd0b05f2f8a01ac9.pdb, chain B (#5), sequence
alignment score = 542.9  
RMSD between 113 pruned atom pairs is 0.589 angstroms; (across all 114 pairs:
0.923)  
  
Matchmaker
38f5286fdff74c2273a65c80f83672790011200005_0000001_08_000000027.pdb, chain B
(#1) with bb890777c74b6c1dcfe34a96719c20f8.pdb, chain B (#6), sequence
alignment score = 542.9  
RMSD between 113 pruned atom pairs is 0.627 angstroms; (across all 114 pairs:
0.940)  
  
Matchmaker
38f5286fdff74c2273a65c80f83672790011200005_0000001_08_000000027.pdb, chain B
(#1) with c7a4f2905fe45902aa7b512475ab2c7e.pdb, chain B (#7), sequence
alignment score = 536.9  
RMSD between 113 pruned atom pairs is 0.618 angstroms; (across all 114 pairs:
0.930)  
  

> sequence align #1/a #2/a

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 228, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 09 Dec 2022 11:05:52
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '69', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file output.fa"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 98, in on_finish  
fasta_output = self.get_file("output.fa")  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'output.fa: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 09 Dec 2022 11:05:52 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'69\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file output.fa"}\'\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 228, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 09 Dec 2022 11:05:53
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '70', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file stdout.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 101, in on_finish  
stdout = self.get_file("stdout.txt")  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stdout.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 09 Dec 2022 11:05:53 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stdout.txt"}\'\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/cmd.py", line 339, in seqalign_align  
realigned = realign_sequences(session, input_sequences, program=program)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 131, in realign_sequences  
job = RealignJob()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 86, in __init__  
self.start(service_name, params, [input_file.name], blocking=True)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 199, in start  
self.session.ui.thread_safe(self.on_finish)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 364, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 104, in on_finish  
raise RuntimeError("No output from %s" % program)  
RuntimeError: No output from Clustal Omega  
  
RuntimeError: No output from Clustal Omega  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 104, in on_finish  
raise RuntimeError("No output from %s" % program)  
  
See log for complete Python traceback.  
  
Webservices job id: SE2W8YZ28WMHH5C1  

> sequence align #1/a, #2/a

Missing or invalid "seqSource" argument: Expected alignment-id or sequences  

> sequence align #1:a, #2:a

Missing or invalid "seqSource" argument: Expected alignment-id or sequences  

> sequence align 1,2

Missing or invalid "seqSource" argument: Expected alignment-id or sequences  

> sequence align #1 #2

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 228, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 09 Dec 2022 11:11:40
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '69', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file output.fa"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 98, in on_finish  
fasta_output = self.get_file("output.fa")  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'output.fa: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 09 Dec 2022 11:11:40 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'69\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file output.fa"}\'\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 228, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 09 Dec 2022 11:11:41
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '70', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file stdout.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 101, in on_finish  
stdout = self.get_file("stdout.txt")  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stdout.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 09 Dec 2022 11:11:41 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stdout.txt"}\'\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/cmd.py", line 339, in seqalign_align  
realigned = realign_sequences(session, input_sequences, program=program)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 131, in realign_sequences  
job = RealignJob()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 86, in __init__  
self.start(service_name, params, [input_file.name], blocking=True)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 199, in start  
self.session.ui.thread_safe(self.on_finish)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 364, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 104, in on_finish  
raise RuntimeError("No output from %s" % program)  
RuntimeError: No output from Clustal Omega  
  
RuntimeError: No output from Clustal Omega  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 104, in on_finish  
raise RuntimeError("No output from %s" % program)  
  
See log for complete Python traceback.  
  
Webservices job id: 1NVYXBR7U6WUJH17  

> sequence align #1/b #2/b

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 228, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 09 Dec 2022 11:11:54
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '69', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file output.fa"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 98, in on_finish  
fasta_output = self.get_file("output.fa")  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'output.fa: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 09 Dec 2022 11:11:54 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'69\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file output.fa"}\'\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 228, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 09 Dec 2022 11:11:55
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '70', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file stdout.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 101, in on_finish  
stdout = self.get_file("stdout.txt")  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stdout.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 09 Dec 2022 11:11:55 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stdout.txt"}\'\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/cmd.py", line 339, in seqalign_align  
realigned = realign_sequences(session, input_sequences, program=program)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 131, in realign_sequences  
job = RealignJob()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 86, in __init__  
self.start(service_name, params, [input_file.name], blocking=True)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 199, in start  
self.session.ui.thread_safe(self.on_finish)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 364, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 104, in on_finish  
raise RuntimeError("No output from %s" % program)  
RuntimeError: No output from Clustal Omega  
  
RuntimeError: No output from Clustal Omega  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 104, in on_finish  
raise RuntimeError("No output from %s" % program)  
  
See log for complete Python traceback.  
  
Webservices job id: 91OQDG52W9ITDIU1  

> toolshed show

Alignment identifier is 1/A  
Alignment identifier is 1  
Alignment identifier is 2/A  
Alignment identifier is 3/A  
Alignment identifier is 4/A  
Alignment identifier is 5/A  
Alignment identifier is 6/A  
Alignment identifier is 7/A  

> sequence align #1/b

Must specify 2 or more protein sequences  

> sequence align #1/a #3/a

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 228, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 09 Dec 2022 11:14:15
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '69', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file output.fa"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 98, in on_finish  
fasta_output = self.get_file("output.fa")  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'output.fa: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 09 Dec 2022 11:14:15 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'69\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file output.fa"}\'\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 660, in get_file  
(data) = self.get_file_with_http_info(job_id, file_name, **kwargs) # noqa:
E501  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api/default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 228, in GET  
return self.request("GET", url,  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/cxservices/rest.py", line 222, in request  
raise ApiException(http_resp=r)  
cxservices.rest.ApiException: (400)  
Reason: Bad Request  
HTTP response headers: HTTPHeaderDict({'Date': 'Fri, 09 Dec 2022 11:14:16
GMT', 'Server': 'Apache/2.4.6 (CentOS)', 'Strict-Transport-Security': 'max-
age=63072000; includeSubdomains; preload', 'Content-Length': '70', 'vary':
'Accept', 'Connection': 'close', 'Content-Type': 'application/json'})  
HTTP response body: b'{"title": "400 Bad Request", "description": "No such
file stdout.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 101, in on_finish  
stdout = self.get_file("stdout.txt")  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/webservices/cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stdout.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 09 Dec 2022 11:14:16 GMT\', \'Server\':
\'Apache/2.4.6 (CentOS)\', \'Strict-Transport-Security\': \'max-age=63072000;
includeSubdomains; preload\', \'Content-Length\': \'70\', \'vary\':
\'Accept\', \'Connection\': \'close\', \'Content-Type\':
\'application/json\'})\nHTTP response body: b\'{"title": "400 Bad Request",
"description": "No such file stdout.txt"}\'\n'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/cmd.py", line 339, in seqalign_align  
realigned = realign_sequences(session, input_sequences, program=program)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 131, in realign_sequences  
job = RealignJob()  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 86, in __init__  
self.start(service_name, params, [input_file.name], blocking=True)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 199, in start  
self.session.ui.thread_safe(self.on_finish)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 364, in thread_safe  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 104, in on_finish  
raise RuntimeError("No output from %s" % program)  
RuntimeError: No output from Clustal Omega  
  
RuntimeError: No output from Clustal Omega  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/align.py", line 104, in on_finish  
raise RuntimeError("No output from %s" % program)  
  
See log for complete Python traceback.  
  
Webservices job id: VYHPJNVBM6TKQBWL  




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Model Number: Z14X000EFCH/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 64 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0.1 (22A400)
      Kernel Version: Darwin 22.1.0
      Time since boot: 11分钟32秒钟

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[Eric Pettersen]

The report is from the realignment web service, but it is happening for Modeller too and I'm guessing all web services. Reproduce with:

open 1mtx
seq align #1.1/a #1.2/a

[Zach Pearson]

This is happening because the clustalo webservice is writing files that Apache can't read.

When I (successfully) tried to reproduce the error, I got the job ID HMUZX2CSI3QEYNUI

>>> ls -lah /var/tmp/cxwebservices/HMUZX2CSI3QEYNUI
total 3.0K
drwxr-s--x.   2 apache ferrin    2 Dec 12 10:42 .
drwxrws---. 259 apache ferrin 1.1K Dec 12 10:42 ..
-rw-r-----.   1 apache ferrin  100 Dec 12 10:42 input.fa
-rw-r-----.   1 root   ferrin   98 Dec 12 10:42 output.fa

I looked inside the worker script at /usr/local/www/webservices/wsgi-scripts/cxservices/cxservices/worker.py and indeed I had commented out the block of code that makes rq workers run as apache-ferrin. D'oh!

I restarted apache and the rq workers after uncommenting the code and re-ran the job, and it succeeded. Please reopen if you find this still happens for another webservice.

[Eric Pettersen]

Works for Modeller too. Thanks!