Xmipp Junk Sorting Issues
Added by Anand Gupta over 12 years ago
We're running a sort junk job on our cluster as part of stack processing, and running into an issue in opening Imagic Files. It looks like appion can't open part of the stack file? It seems to be able to open up almost 50% of the particles...
The stack file was generated through appion build stack pipeline...
The log and job file are attached.
Traceback (most recent call last):
File "/programs/m/appion/2.2/sortJunkStack.py", line 154, in <module>
sortJunk.start()
File "/programs/m/appion/2.2/sortJunkStack.py", line 50, in start
apXmipp.breakupStackIntoSingleFiles(fn_oldstack)
File "/programs/i386-mac/python/2.7/lib/python2.7/site-packages/appionlib/apXmipp.py", line 130, in breakupStackIntoSingleFiles
breaker.start(stackfile)
File "/programs/i386-mac/python/2.7/lib/python2.7/site-packages/appionlib/apImagicFile.py", line 837, in start
stackdata = readImagic(stackfile, first=first, last=last, msg=False)
File "/programs/i386-mac/python/2.7/lib/python2.7/site-packages/appionlib/apImagicFile.py", line 163, in readImagic
images = readImagicData(datafilename, headerdict, first, numpart)
File "/programs/i386-mac/python/2.7/lib/python2.7/site-packages/appionlib/apImagicFile.py", line 239, in readImagicData
f.seek(partbytes*(firstpart-1))
IOError: [Errno 22] Invalid argument
| sortjunk11.appionsub.log (4.44 KB) sortjunk11.appionsub.log | Log File | ||
| sortjunk11.appionsub.job (365 Bytes) sortjunk11.appionsub.job | Job File |
Replies (2)
RE: Xmipp Junk Sorting Issues - Added by Amber Herold over 12 years ago
The message means that it is trying to read a particle in a file location that can't be found.
Try viewing the stack that you are trying to read within Appion or Imagic to make sure the particles can be seen. If not, there was a problem writing the particles to the stack.
RE: Xmipp Junk Sorting Issues - Added by Anand Gupta over 12 years ago
We can open the stack in Appion and view all particles without any issue. In addition, we're able to run the same job to completion on a single computer outside of our cluster, albeit rather slowly. Any ideas on other places that error could come from? The versions of a bunch of Appion dependencies are different between the cluster and single machine...