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#7705 closed defect (fixed)

Web services not starting

Reported by:	tharikadilhari@…	Owned by:	Greg Couch
Priority:	critical	Milestone:
Component:	Web Services	Version:
Keywords:		Cc:	chimera-programmers, Scooter Morris
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.19042
ChimeraX Version: 1.5.dev202209281710 (2022-09-28 17:10:28 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5.dev202209281710 (2022-09-28)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5TTU

5ttu title:  
Jak3 with covalent inhibitor 7 [more info...]  
  
Chain information for 5ttu #1  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase JAK3 | JAK3_HUMAN  
  
Non-standard residues in 5ttu #1  
---  
7KV —
1-[(3aR,7aR)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)octahydro-6H-pyrrolo[2,3-c]pyridin-6-yl]propan-1-one  
SO4 — sulfate ion  
  

> select coil

569 atoms, 565 bonds, 2 pseudobonds, 76 residues, 2 models selected  

> color (#!1 & sel) yellow

> select helix

1167 atoms, 1185 bonds, 144 residues, 1 model selected  

> color sel cornflower blue

> select strand

407 atoms, 402 bonds, 51 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel peach puff

> select ::name="7KV"

22 atoms, 25 bonds, 1 residue, 1 model selected  

> color sel lime

> select ::name="7KV"

22 atoms, 25 bonds, 1 residue, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:830

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:830-834

13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected  

> ui tool show "Model Loops"

> modeller refine 1/A:1:27-31 numModels 5 fast false adjacentFlexible 1
> protocol DOPE-HR

Webservices job id: QZYXYLN1DYUWZS5X  

> ui tool show "Model Panel"

> select /A:829-830

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:829-835

23 atoms, 21 bonds, 1 pseudobond, 4 residues, 2 models selected  

> select /A:830

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:830-834

13 atoms, 11 bonds, 1 pseudobond, 2 residues, 2 models selected  

> color (#!1 & sel) red

> ui tool show "Model Loops"

> modeller refine 1/A:1:all-missing numModels 5 fast true adjacentFlexible 1
> protocol DOPE-HR

Webservices job id: XL1I781PTHGZ0RXE  

> ui tool show "Modeller Comparative"

> modeller comparative 1/A:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false

Webservices job id: 3JVZWGOE6NPTSQEV  

> select ::name="7KV"

22 atoms, 25 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel intraMol false intraRes false reveal true

3 hydrogen bonds found  

> select clear

> transparency 50

> select ::name="7KV"

22 atoms, 25 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel intraMol false intraRes false reveal true

3 hydrogen bonds found  

> select sequence LVAVKQLQHS

73 atoms, 72 bonds, 10 residues, 1 model selected  

> select

2405 atoms, 2226 bonds, 6 pseudobonds, 504 residues, 3 models selected  

> surface hidePatches (#!1 & sel)

> ui tool show Distances

> select /A:826

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  

> select /A:877

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:877

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select
> /A:818-820,861-877,909-943,951-953,990-1002,1006-1022,1025-1038,1045-1056,1067-1078,1081-1085,1087-1099

1167 atoms, 1185 bonds, 144 residues, 1 model selected  

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  

> select clear

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  
No distances to delete!  
Exactly two atoms must be selected!  

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  

> select /A:822-829,835-841,850-953,955-959,962-965,972-973,980-982,1003-1005

1050 atoms, 1059 bonds, 1 pseudobond, 130 residues, 2 models selected  

> select /A:822-829,835-841,850-953,955-959,962-965,972-973,980-982,1003-1005

1050 atoms, 1059 bonds, 1 pseudobond, 130 residues, 2 models selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-1003

1142 atoms, 1164 bonds, 1 pseudobond, 143 residues, 2 models selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-978

949 atoms, 963 bonds, 1 pseudobond, 118 residues, 2 models selected  

> select /A:855-856

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-953

757 atoms, 768 bonds, 1 pseudobond, 93 residues, 2 models selected  

> select /A:855-953

757 atoms, 768 bonds, 1 pseudobond, 93 residues, 2 models selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-978

949 atoms, 963 bonds, 1 pseudobond, 118 residues, 2 models selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-1003

1142 atoms, 1164 bonds, 1 pseudobond, 143 residues, 2 models selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-1003

1142 atoms, 1164 bonds, 1 pseudobond, 143 residues, 2 models selected  

> select /A:856-857

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:856-888

270 atoms, 274 bonds, 33 residues, 1 model selected  

> select /A:863-864

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:829-864

236 atoms, 237 bonds, 1 pseudobond, 33 residues, 2 models selected  

> select /A:855-879

203 atoms, 205 bonds, 25 residues, 1 model selected  

> select /A:855-1004

1153 atoms, 1176 bonds, 1 pseudobond, 144 residues, 2 models selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-980

969 atoms, 984 bonds, 1 pseudobond, 120 residues, 2 models selected  

> view sel

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  

> ui tool show Distances

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-1053

1505 atoms, 1536 bonds, 2 pseudobonds, 188 residues, 2 models selected  

> select /A:855-856

18 atoms, 17 bonds, 2 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:857

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:857-1058

1526 atoms, 1557 bonds, 2 pseudobonds, 191 residues, 2 models selected  

> select /A:857

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:857-1099

1838 atoms, 1883 bonds, 2 pseudobonds, 232 residues, 2 models selected  

> select /A:857-1099

1838 atoms, 1883 bonds, 2 pseudobonds, 232 residues, 2 models selected  
Exactly two atoms must be selected!  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-885

252 atoms, 255 bonds, 31 residues, 1 model selected  

> select /A:855-1053

1505 atoms, 1536 bonds, 2 pseudobonds, 188 residues, 2 models selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-879

203 atoms, 205 bonds, 25 residues, 1 model selected  

> select /A:855-879

203 atoms, 205 bonds, 25 residues, 1 model selected  

> select /A:855-879

203 atoms, 205 bonds, 25 residues, 1 model selected  

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select
> /A:822-829,835-841,850-856,886-890,899-903,945-946,955-959,962-965,972-973,980-982,1003-1005

407 atoms, 402 bonds, 51 residues, 1 model selected  

> select /A:822-928,945-946,955-959,962-965,972-973,980-982,1003-1005

930 atoms, 937 bonds, 2 pseudobonds, 117 residues, 2 models selected  

> select /A:822-1028

1573 atoms, 1604 bonds, 2 pseudobonds, 198 residues, 2 models selected  

> select clear

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select clear

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select clear

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-1053

1505 atoms, 1536 bonds, 2 pseudobonds, 188 residues, 2 models selected  

> select clear

> select /A:855-1053

1505 atoms, 1536 bonds, 2 pseudobonds, 188 residues, 2 models selected  

> select clear

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855-1028

1351 atoms, 1380 bonds, 1 pseudobond, 168 residues, 2 models selected  

> select clear

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:841,855

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A:841,855-1099

1868 atoms, 1913 bonds, 2 pseudobonds, 235 residues, 2 models selected  

> select clear

> select /A:841,855-1099

1868 atoms, 1913 bonds, 2 pseudobonds, 235 residues, 2 models selected  

> select clear

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:841,855

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A:841-855

107 atoms, 108 bonds, 15 residues, 1 model selected  

> select /A:841-1053

1603 atoms, 1636 bonds, 2 pseudobonds, 202 residues, 2 models selected  

> select /A:843-844

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:844-1030

1435 atoms, 1465 bonds, 1 pseudobond, 181 residues, 2 models selected  
Either three or four atoms must be selected!  

> select clear

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:841,855

21 atoms, 20 bonds, 2 residues, 1 model selected  
Either three or four atoms must be selected!  

> select /A:886

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A:886

12 atoms, 12 bonds, 1 residue, 1 model selected  
Either three or four atoms must be selected!  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:855,886

21 atoms, 20 bonds, 2 residues, 1 model selected  

> select /A:841,855,886

33 atoms, 32 bonds, 3 residues, 1 model selected  
Either three or four atoms must be selected!  

> save C:/Users/Dilshan/Desktop/ADRB_loop.pdb relModel #1

> cartoon hide sel

> select :828-

Expected an objects specifier or a keyword  

> 836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9

Unknown command:
836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9  

> 05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004

Unknown command:
05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004  

> select :828-

Expected an objects specifier or a keyword  

> 836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9

Unknown command:
836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9  

> 05:908:909:911:912:948:949:953:954:956:966-972:981:983-

Unknown command: 05:908:909:911:912:948:949:953:954:956:966-972:981:983-  

> 990:994:1004

Unknown command: 990:994:1004  

> select
> :828-836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9

167 atoms, 156 bonds, 1 pseudobond, 21 residues, 2 models selected  

> 05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004

Unknown command:
05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004  

> select:828-836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9

Unknown command:
select:828-836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:9  

> 05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004

Unknown command:
05:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004  

> select
> :828-836:853:855:857:863:864:867:868:870:871:874:875:884:900:902:904:905:908:909:911:912:948:949:953:954:956:966-972:981:983-990:994:1004

379 atoms, 363 bonds, 1 pseudobond, 49 residues, 2 models selected  

> surface (#!1 & sel)

> select

2405 atoms, 2226 bonds, 6 pseudobonds, 504 residues, 3 models selected  

> hide sel atoms

> hide sel cartoons

> hide sel surfaces

> select ::name="7KV"

22 atoms, 25 bonds, 1 residue, 1 model selected  

> select sel :< 5

175 atoms, 159 bonds, 3 pseudobonds, 30 residues, 2 models selected  

> select sel :< 4.5

2216 atoms, 511 bonds, 4 pseudobonds, 315 residues, 3 models selected  

> style sel stick

Changed 2216 atom styles  

> show sel atoms

> show sel surfaces

> ui tool show "Measure Volume and Area"

QWindowsWindow::setGeometry: Unable to set geometry 1366x726+0+23 (frame:
1382x765-8-8) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1366x705+0+23 (frame: 1382x744-8-8) margins: 8, 31, 8, 8
minimum size: 472x726 MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0,
y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=488, y=765)))  

> close session

Modeller job (ID 3JVZWGOE6NPTSQEV) finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api\default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api  
response_data = self.request(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\cxservices\rest.py",
line 228, in GET  
return self.request("GET", url,  
File "C:\Program Files\ChimeraX\bin\lib\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, 30 Sep 2022 18:59:57
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 stderr.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 661, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\modeller\common.py", line 563, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 18:59:57 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 stderr.txt"}\'\n'  
  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 18:59:57 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 stderr.txt"}\'\n'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
  
See log for complete Python traceback.  
  
Modeller job (ID QZYXYLN1DYUWZS5X) finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api\default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api  
response_data = self.request(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\cxservices\rest.py",
line 228, in GET  
return self.request("GET", url,  
File "C:\Program Files\ChimeraX\bin\lib\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, 30 Sep 2022 18:59:59
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 stderr.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 661, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\modeller\common.py", line 563, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 18:59:59 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 stderr.txt"}\'\n'  
  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 18:59:59 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 stderr.txt"}\'\n'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
  
See log for complete Python traceback.  
  
Modeller job (ID XL1I781PTHGZ0RXE) finished  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 218, in get_file  
content = self.chimerax_api.get_file(self.job_id, filename)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api\default_api.py", line 726, in get_file_with_http_info  
return self.api_client.call_api(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 316, in call_api  
return self.__call_api(resource_path, method,  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 148, in __call_api  
response_data = self.request(  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\cxservices\api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\cxservices\rest.py",
line 228, in GET  
return self.request("GET", url,  
File "C:\Program Files\ChimeraX\bin\lib\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, 30 Sep 2022 19:00:00
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 stderr.txt"}'  
  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 661, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\modeller\common.py", line 563, in on_finish  
err = self.get_file("stderr.txt")  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 19:00:00 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 stderr.txt"}\'\n'  
  
KeyError: 'stderr.txt: (400)\nReason: Bad Request\nHTTP response headers:
HTTPHeaderDict({\'Date\': \'Fri, 30 Sep 2022 19:00:00 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 stderr.txt"}\'\n'  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\webservices\cxservices_job.py", line 220, in get_file  
raise KeyError("%s: %s" % (filename, str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.13399 Core Profile Forward-Compatible Context 15.201.1151.0
OpenGL renderer: AMD Radeon HD 6310 Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: en_GB.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: TOSHIBA
Model: Satellite C855D
OS: Microsoft Windows 10 Pro (Build 19042)
Memory: 6,007,668,736
MaxProcessMemory: 137,438,953,344
CPU: 2 AMD E-300 APU with Radeon(tm) HD Graphics
OSLanguage: en-GB

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    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: 1.41.3
    ChimeraX-AtomicLibrary: 8.0.1
    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: 1.0.2
    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.dev202209281710
    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: 1.8.1
    ChimeraX-Map: 1.1.1
    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: 2.1
    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
    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: 2.6.7
    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: 1.24.1
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    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
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.0
    filelock: 3.7.1
    fonttools: 4.37.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 4.12.0
    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: 4.11.1
    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: 1.5.5
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    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: 2022.2.1
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    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: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.8.1

Change History (7)

comment:1 by Eric Pettersen, 3 years ago

Cc:	chimera-programmers added
Component:	Unassigned → Web Services
Owner:	set to Zach Pearson
Platform:	→ all
Priority:	normal → critical
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Web services not starting

If you start any web service job from ChimeraX, the corresponding directory in /var/tmp/cxwebservices does not get created.

Reported by Tharika Dilhari

comment:2 by Zach Pearson, 3 years ago

huh, rq says we have 0 workers online.

comment:3 by Zach Pearson, 3 years ago

Cc:	Scooter Morris added
Owner:	changed from Zach Pearson to Greg Couch

Greg or Scooter:

Can one of you copy /usr/local/etc/init.d/rq_workers from a node that has that script to Watson and Franklin, neither of which have it? We need to put it back to get our webservice jobs running (the current backlog is 89 jobs).

Not sure what happened to it.

comment:4 by Greg Couch, 3 years ago

/usr/local/etc/init.d/rq_workers is not on any plato node.

comment:5 by Greg Couch, 3 years ago

FYI, restarting the webservices resource appears to have fixed the problem. Please confirm.

comment:6 by Eric Pettersen, 3 years ago

Yes, I can run blast from ChimeraX now.

comment:7 by Greg Couch, 3 years ago

Resolution:	→ fixed
Status:	assigned → closed

Great. Glad to hear that it works now.

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