[scipion-users] Error trying to start reconstructions.

[Dennis T. <dt...@pr...>]

Hi,

When I reach the point of doing initial reconstructions after aligning 
with xmipp cl2d and classifiying with xmipp cl2d and select "good" 
particles. I get failures when running EMAN easy refine and Xmipp 
projection matching.

Below are the error messages for each:

using xmipp projection matching it fails with the following error

:   Traceback (most recent call last):
00467:     File "/opt/scipion/pyworkflow/protocol/protocol.py", line 
167, in run
00468:       self._run()
00469:     File "/opt/scipion/pyworkflow/protocol/protocol.py", line 
211, in _run
00470:       resultFiles = self._runFunc()
00471:     File "/opt/scipion/pyworkflow/protocol/protocol.py", line 
207, in _runFunc
00472:       return self._func(*self._args)
00473:     File 
"/opt/scipion/pyworkflow/em/packages/xmipp3/protocol_projmatch/protocol_projmatch.py", 
line 202, in filterVolumeStep
00474:       runFilterVolumeStep(self, iterN, refN, 
constantToAddToFiltration, **kwargs)
00475:     File 
"/opt/scipion/pyworkflow/em/packages/xmipp3/protocol_projmatch/projmatch_steps.py", 
line 665, in runFilterVolumeStep
00476:       if (filterInPxAt > 0.5):
00477:   UnboundLocalError: local variable 'filterInPxAt' referenced 
before assignment
00478:   Protocol failed: local variable 'filterInPxAt' referenced 
before assignment
00479:   FAILED: filterVolumeStep, step 18
00480:     2017-03-01 09:38:58.098115
00481:   Cleaning temporarly files....
00482:   ------------------- PROTOCOL FAILED (DONE 18/36)

Using EMAN2 easy process I get the following errors

01507:   executing  e2simmx.py refine_01/projections_02_even.hdf 
refine_01/projections_02_even.hdf refine_01/proj_simmx_02_even.hdf 
--shrink=2 --align=rotate_translate_flip --aligncmp=sqeuclidean:normto=1 
--cmp=sqeuclidean --saveali --force --verbose=-1 --parallel=thread:30
01508:   in check
01509:   Matrix size 76 x 76 into 96 regions ->   11 x 8 blocks -> 88 
subprocesses (6 x 9 each)
01510:   87/88
01511:   88  tasks submitted
01512:
01513:   All simmx tasks complete
01514:   Cleaning up thread server. Please wait.
01515:   Finding 24 dissimilar classification centers
01516:   Sort references
01517:   Associating references with centers
01518:   Averaging each center
01519:   Traceback (most recent call last):
01520:     File 
"/opt/scipion/software/em/eman2.12/bin/e2simmx2stage.py", line 235, in 
<module>
01521:       main()
01522:     File 
"/opt/scipion/software/em/eman2.12/bin/e2simmx2stage.py", line 147, in main
01523:       avg=EMData(args[0],i[0])
01524:   IndexError: list index out of range
01525:   Error running:  e2simmx2stage.py 
refine_01/projections_02_even.hdf sets/inputSet_even.lst 
refine_01/simmx_02_even.hdf refine_01/proj_simmx_02_even.hdf 
refine_01/proj_stg1_02_even.hdf refine_01/simmx_stg1_02_even.hdf 
--saveali --cmp frc:snrweight=1:maxres=14.0     --align 
rotate_translate_flip --aligncmp ccc --ralign refine --raligncmp ccc 
--shrinks1 2   --mask refine_01/simmask.hdf  --parallel thread:30
01526:   Traceback (most recent call last):
01527:     File "/opt/scipion/pyworkflow/protocol/protocol.py", line 
167, in run
01528:       self._run()
01529:     File "/opt/scipion/pyworkflow/protocol/protocol.py", line 
211, in _run
01530:       resultFiles = self._runFunc()
01531:     File "/opt/scipion/pyworkflow/protocol/protocol.py", line 
207, in _runFunc
01532:       return self._func(*self._args)
01533:     File 
"/opt/scipion/pyworkflow/em/packages/eman2/protocol_refineasy.py", line 
274, in refineStep
01534:       self.runJob(program, args, cwd=self._getExtraPath())
01535:     File "/opt/scipion/pyworkflow/protocol/protocol.py", line 
960, in runJob
01536:       self._stepsExecutor.runJob(self._log, program, arguments, 
**kwargs)
01537:     File "/opt/scipion/pyworkflow/protocol/executor.py", line 56, 
in runJob
01538:       env=env, cwd=cwd)
01539:     File "/opt/scipion/pyworkflow/utils/process.py", line 51, in 
runJob
01540:       return runCommand(command, env, cwd)
01541:     File "/opt/scipion/pyworkflow/utils/process.py", line 65, in 
runCommand
01542:       check_call(command, shell=True, stdout=sys.stdout, 
stderr=sys.stderr, env=env, cwd=cwd)
01543:     File "/opt/scipion/software/lib/python2.7/subprocess.py", 
line 540, in check_call
01544:       raise CalledProcessError(retcode, cmd)
01545:   CalledProcessError: Command 
'/opt/scipion/software/em/eman2.12/Python/bin/python 
/opt/scipion/software/em/eman2.12/bin/e2refine_easy.py 
--input=sets/inputSet.lst 
--model=../../000970_XmippProtFilterVolumes/extra/output_volume.vol 
--targetres=14.000000 --speed=5 --sym=d2 --iter=4 --mass=150.000000 
--apix=2.100000 --classkeep=0.900000 --m3dkeep=1.000000 
--parallel=thread:30 --threads=30 --classrefsf 
--m3dpostprocess=filter.lowpass.gauss' returned non-zero exit status 1
01546:   Protocol failed: Command 
'/opt/scipion/software/em/eman2.12/Python/bin/python 
/opt/scipion/software/em/eman2.12/bin/e2refine_easy.py 
--input=sets/inputSet.lst 
--model=../../000970_XmippProtFilterVolumes/extra/output_volume.vol 
--targetres=14.000000 --speed=5 --sym=d2 --iter=4 --mass=150.000000 
--apix=2.100000 --classkeep=0.900000 --m3dkeep=1.000000 
--parallel=thread:30 --threads=30 --classrefsf 
--m3dpostprocess=filter.lowpass.gauss' returned non-zero exit status 1
01547:   FAILED: refineStep, step 2
01548:     2017-02-28 18:49:02.599250
01549:   Cleaning temporarly files....
01550:   ------------------- PROTOCOL FAILED (DONE 2/3)


-- 
Dr. Dennis Thomas
Cryo-EM Facility Manager
Center for Integrative Proteomics Research
Rutgers University
Phone: 848-445-5302