Opened 5 years ago

Closed 5 years ago

#4455 closed defect (can't reproduce)

BLAST failure

Reported by: kiernan1@… Owned by: pett
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-05-03)
Description
I used the BLAST Protein function and got this error. 

Log:
Startup Messages  
---  
note | Updating list of available bundles failed: Internal Server Error  
  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

libpng warning: iCCP: known incorrect sRGB profile  

UCSF ChimeraX version: 0.9 (2019-05-03)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Kaitlyn/Documents/Cryo-EM/Cas9 structures/Product-reb7-Cas9
only.pdb"

Summary of feedback from opening /Users/Kaitlyn/Documents/Cryo-EM/Cas9
structures/Product-reb7-Cas9 only.pdb  
---  
warnings | Ignored bad PDB record found on line 20  
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2  
  
Ignored bad PDB record found on line 21  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 22  
BOND : 0.008 0.065 11811  
  
Ignored bad PDB record found on line 23  
ANGLE : 0.786 9.688 16734  
  
Ignored bad PDB record found on line 24  
CHIRALITY : 0.049 0.296 2030  
  
16 messages similar to the above omitted  
  
Chain information for Product-reb7-Cas9 only.pdb #1  
---  
Chain | Description  
A | No description available  
  

> style selAtoms sphere

Changed 8100 atom styles  

> style selAtoms stick

Changed 8100 atom styles  

> toolshed show "Modeller Comparative"

> undo

> toolshed show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 toolId
7

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: appBlastProtein2Service16175583085371107483065  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service16175583085371107483065  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 320, in fetch_from_pdb  
f = urlopen(url)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 222, in urlopen  
return opener.open(url, data, timeout)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 531, in open  
response = meth(req, response)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 641, in http_response  
'http', request, response, code, msg, hdrs)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 569, in error  
return self._call_chain(*args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 649, in http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 544, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 101, in on_finish  
self.tool.job_finished(self, p, self._params())  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 185, in job_finished  
self._show_results(job.atomspec, blast_results)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 218, in _show_results  
self._add_pdbinfo(pdb_chains)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 236, in _add_pdbinfo  
data = info.fetch_info(self.session, chain_ids)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 47, in fetch_info  
xml = fetch_from_pdb(session, 'describePDB', set(pdb_ids))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 323, in fetch_from_pdb  
except (URLError, HTTPError) as e:  
NameError: name 'HTTPError' is not defined  
  
NameError: name 'HTTPError' is not defined  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 323, in fetch_from_pdb  
except (URLError, HTTPError) as e:  
  
See log for complete Python traceback.  
  

> select #1.1

5 pseudobonds, 1 model selected  

> ~select #1.1

Nothing selected  

> select #1

8100 atoms, 8253 bonds, 5 pseudobonds, 1 model selected  

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 toolId
7

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: appBlastProtein2Service1617558365126895884501  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1617558365126895884501  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 320, in fetch_from_pdb  
f = urlopen(url)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 222, in urlopen  
return opener.open(url, data, timeout)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 531, in open  
response = meth(req, response)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 641, in http_response  
'http', request, response, code, msg, hdrs)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 569, in error  
return self._call_chain(*args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 649, in http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 544, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 101, in on_finish  
self.tool.job_finished(self, p, self._params())  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 185, in job_finished  
self._show_results(job.atomspec, blast_results)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 218, in _show_results  
self._add_pdbinfo(pdb_chains)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 236, in _add_pdbinfo  
data = info.fetch_info(self.session, chain_ids)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 47, in fetch_info  
xml = fetch_from_pdb(session, 'describePDB', set(pdb_ids))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 323, in fetch_from_pdb  
except (URLError, HTTPError) as e:  
NameError: name 'HTTPError' is not defined  
  
NameError: name 'HTTPError' is not defined  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 323, in fetch_from_pdb  
except (URLError, HTTPError) as e:  
  
See log for complete Python traceback.  
  

> toolshed show "Modeller Comparative"

> select /A

8100 atoms, 8253 bonds, 5 pseudobonds, 1 model selected  

> show #1 target m

> select down

8100 atoms, 8253 bonds, 5 pseudobonds, 1 model selected  

> select sequence 1-1368

Nothing selected  

> select down

Nothing selected  

> select up

Nothing selected  

> select sequence 1-1366

Nothing selected  

> select sequence 1-1300

Nothing selected  

> select sequence 10-1366

Nothing selected  

> show #1 target m

> show #1 target m

> select sequence 10-1366

Nothing selected  

> select sequence 30-60

Nothing selected  

> select sequence 30-60

Nothing selected  

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

Incomplete command: sequence  

> select

8100 atoms, 8253 bonds, 5 pseudobonds, 1 model selected  

> toolshed show "Blast Protein"

> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 toolId
9

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: appBlastProtein2Service1617558982109-55847901  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1617558982109-55847901  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 320, in fetch_from_pdb  
f = urlopen(url)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 222, in urlopen  
return opener.open(url, data, timeout)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 531, in open  
response = meth(req, response)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 641, in http_response  
'http', request, response, code, msg, hdrs)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 569, in error  
return self._call_chain(*args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 503, in _call_chain  
result = func(*args)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/urllib/request.py",
line 649, in http_error_default  
raise HTTPError(req.full_url, code, msg, hdrs, fp)  
urllib.error.HTTPError: HTTP Error 404: Not Found  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 544, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 101, in on_finish  
self.tool.job_finished(self, p, self._params())  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 185, in job_finished  
self._show_results(job.atomspec, blast_results)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 218, in _show_results  
self._add_pdbinfo(pdb_chains)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 236, in _add_pdbinfo  
data = info.fetch_info(self.session, chain_ids)  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 47, in fetch_info  
xml = fetch_from_pdb(session, 'describePDB', set(pdb_ids))  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 323, in fetch_from_pdb  
except (URLError, HTTPError) as e:  
NameError: name 'HTTPError' is not defined  
  
NameError: name 'HTTPError' is not defined  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 323, in fetch_from_pdb  
except (URLError, HTTPError) as e:  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by pett, 5 years ago

Component: Unassigned → Sequence
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → BLAST failure

comment:2 by pett, 5 years ago

Resolution: → can't reproduce
Status: accepted → closed

Hi Kaitlyn,

This failure may have been a temporary problem with our servers. It will likely work if you try again. Nonetheless, I highly recommend you get the ChimeraX daily build because the BLAST tool has many bug fixes and improvements in the daily build compared to the 0.9 release that you are running.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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