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#2917 closed defect (fixed)

BlaST web service: No alias or index file found for protein database

Reported by:	petevseev@…	Owned by:	Conrad Huang
Priority:	normal	Milestone:
Component:	Sequence	Version:
Keywords:		Cc:	noemi.ruiz@…
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.92 (2020-03-03)
Description
Blastprotein does not work :(
blastprotein 1
Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr or pdb for sequences similar to the given protein sequence Opal service URL: http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service Opal job id: appBlastProtein2Service15833070227471984832818 Opal status URL prefix: http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833070227471984832818 stdout.txt = standard output stderr.txt = standard error BlastProtein finished. Traceback (most recent call last):   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 606, in customEvent     func(*args, **kw)   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\blastprotein\job.py", line 96, in on_finish     p = Parser("query", self.seq, results)   File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\blastprotein\blastp_parser.py", line 47, in __init__     tree = ET.fromstring(output)   File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316, in XML     return parser.close()   File "<string>", line None xml.etree.ElementTree.ParseError: no element found: line 1, column 0 File "", line None
xml.etree.ElementTree.ParseError: no element found: line 1, column 0

File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316, in XML
return parser.close()

See log for complete Python traceback.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.92 (2020-03-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:/Users/Peter/Downloads/05-modeller/05-modeller/076-tail sheath
> protein.fasta"

Summary of feedback from opening
C:/Users/Peter/Downloads/05-modeller/05-modeller/076-tail sheath protein.fasta  
---  
note | Alignment identifier is 076-tail sheath protein.fasta  
  
Opened 1 sequences from 076-tail sheath protein.fasta  

> blastprotein 1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service15833067449811830343188  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833067449811830343188  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 606, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 96, in on_finish  
p = Parser("query", self.seq, results)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\blastp_parser.py", line 47, in __init__  
tree = ET.fromstring(output)  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
File "<string>", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
  
See log for complete Python traceback.  
  

> blastprotein 1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1583306829274-1619047780  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1583306829274-1619047780  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 606, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 96, in on_finish  
p = Parser("query", self.seq, results)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\blastp_parser.py", line 47, in __init__  
tree = ET.fromstring(output)  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
File "<string>", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
  
See log for complete Python traceback.  
  

> blastprotein 1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service15833068734461897175413  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833068734461897175413  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 606, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 96, in on_finish  
p = Parser("query", self.seq, results)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\blastp_parser.py", line 47, in __init__  
tree = ET.fromstring(output)  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
File "<string>", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
  
See log for complete Python traceback.  
  

> toolshed show "Blast Protein"

> blastprotein 1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1583307009054-562103175  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1583307009054-562103175  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 606, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 96, in on_finish  
p = Parser("query", self.seq, results)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\blastp_parser.py", line 47, in __init__  
tree = ET.fromstring(output)  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
File "<string>", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
  
See log for complete Python traceback.  
  

> blastprotein 1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service15833070227471984832818  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service15833070227471984832818  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 606, in customEvent  
func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\job.py", line 96, in on_finish  
p = Parser("query", self.seq, results)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\blastprotein\blastp_parser.py", line 47, in __init__  
tree = ET.fromstring(output)  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
File "<string>", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "", line None  
xml.etree.ElementTree.ParseError: no element found: line 1, column 0  
  
File "C:\Program Files\ChimeraX\bin\lib\xml\etree\ElementTree.py", line 1316,
in XML  
return parser.close()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 441.41
OpenGL renderer: GeForce GTX 1060 with Max-Q Design/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (5)

comment:1 by Eric Pettersen, 6 years ago

Component:	Unassigned → Sequence
Owner:	set to Conrad Huang
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → BlaST web service: No alias or index file found for protein database

Blast protein broken for both Chimera and ChimeraX

comment:2 by Eric Pettersen, 6 years ago

Cc:	noemi.ruiz@… added

comment:3 by Conrad Huang, 6 years ago

Once again, the PDB BLAST databases got wiped out by the broken BLAST nightly updates. I have rewritten the BLAST update script so that it uses a different mechanism that works (appears to work) with the v5 BLAST databases that NCBI now publishes.

Leaving this ticket until next week to make sure that the new update script works properly.

in reply to: 4 ; follow-up: 4 comment:4 by petevseev@…, 6 years ago

Thank you very much for your support.

If you need testers - I'm always ready to assist you!

чт, 5 мар. 2020 г. в 21:11, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>:

comment:5 by Conrad Huang, 5 years ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed in b62257089.

Instead of catching one specific exception raised while parsing data from server, we now catch all of them and report an error instead of a traceback.

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