Cannot start tomogram preprocessing

[Jaime Llodra]

Dear Members of this group,

I want to preprocess a stack of tiff images for segmentation and when I press launch I get the following message.

TUAP227:EMAN2_test jl2235$ e2projectmanager.py

Newpath: /Users/jl2235/Desktop/EMAN2_test

NOT Writing notes, ppid=-2

1/1Traceback (most recent call last):

  File "/Users/jl2235/System/Applications/bin/e2tomoseg_preproc.py", line 86, in <module>

    main()

  File "/Users/jl2235/System/Applications/bin/e2tomoseg_preproc.py", line 83, in main

    im.write_image(procout[0],0)

  File "/Users/jl2235/System/Applications/lib/python3.7/site-packages/EMAN2.py", line 2763, in db_write_image

    return self.write_image_c(fsp, *parms)

RuntimeError: FileAccessException at /Users/eman/miniconda3/conda-bld/eman2_1626370085625/work/libEM/io/hdfio2.cpp:471: error with 'tomograms/stack_preproc.hdf': 'cannot access file 'tomograms/stack_preproc.hdf'' caught

Any idea what is wrong?

Thanks in advance for any idea/suggestion

Jaime Llodra

[Ludtke, Steven J.]

Hi Jaime,

the error is fairly self-explanatory if you read it:

FileAccessException

tomograms/stack_preproc.hdf

this means a program tried to read that file, and the computer denied access. Have you run all of the processing using the same user account? If, for example, you did some testing when logged in as a system administrator then tried to continue processing as an ordinary user, some files may have been created that only the administrator has permission to access. That would  be my best guess. If that doesn't help, send the output from 'ls -al tomograms' and we can take a look.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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[Jaime Llodra]

Good morning Steven,

I solved the problem. I went directly from tomogram to preprocessing bypassing the Import Tomogram step. My fault

Have a good day

Jaime Llodra