error message PGFIO-F-209/OPEN/unit=77/'OLD'

Submitted by adesgeorges on Mon, 2010-08-09 19:40

Forums

Frealign

Hello,

I get this error message at the start of my refinement run (mode 1):
-----------------------------
PGFIO-F-209/OPEN/unit=77/'OLD' specified for file which does not exist.
File name = /master.raid/home_master/hr80_0.par !FINPAR - Input parameter file if mode >=0

In source file card10.f, at line number 54

-----------------------------
The file is definitely there and has all the bits that I think it should have..

By advance, thank you for your help.

niko Mon, 2010-08-09 21:53

Frealign does not have any parser function that would recognize that you have a comment (after the '!') in your input line. Therefore, it is reading your file name as

/master.raid/home_master/hr80_0.par !FINPAR - Input parameter file if mode >=0

Just remove

!FINPAR - Input parameter file if mode >=0

and try again.

adesgeorges Tue, 2010-08-10 12:15

I spoke to quick!

I removed the annotation and it still gives me the exact same error.

MATCHING PROJECTIONS IMAGE STACK ?
hr80_match.spi_89_96
Padding reference volume, IPAD = 4
Interpolation radius for reference IRADA = 0

PGFIO-F-209/OPEN/unit=77/'OLD' specified for file which does not exist.
File name = /master.raid/home_master/frealign_v8.08_2/spiderinput/hr80_0.par

In source file card10.f, at line number 54

niko Tue, 2010-08-10 15:17

You should check again if the file is really there. The best way to to this is to include a line in your script before calling Frealign, such as

ls /master.raid/home_master/frealign_v8.08_2/spiderinput/hr80_0.par

and then check that the file is actually listed when you run the script. This avoids errors where one character in a file name is wrong and, therefore, the file cannot be found.

adesgeorges Tue, 2010-08-10 16:55

I did check, it is really there! :-)

Is it the usual error that you get when a file is missing?

Is it only the alignment file or does it need to have the cards as header? That would explain..

What is the card 10f otherwise?

niko Tue, 2010-08-10 17:32

card10 is the part of Frealign that reads in your particle alignment parameters (angles, shifts etc.). It asks for a file name for the parameter file. The error you get is a low-level Fortran error, which means it is probably nothing to do with the code in card10. Have you deleted all the trailing spaces in the line in your script that contains the file name? I really cannot think of any other reason you are getting this error. If the input line really only contains the file name (no spaces or other characters at the beginning or end of the line) maybe you could paste the script in your reply for me to look at.

rdrighetto Wed, 2015-10-28 14:15

Hi,

I want to point out that I am getting the same error message when attempting refinement with classification.
I am running V9.11 - 12.10.15.

What I have realized is that when refining (MODE 1) with more than 1 reference, FREALIGN renames my .par and .mrc files from the previous cycle M to something like ProjectName_M.par and ProjectName_M.mrc.
Then when refining it looks for ProjectName_M_rN.par and ProjectName_M_rN.mrc (where N is any within the number of references specified for the M+1 cycle) files in the project folder, but they do not exist.
These ProjectName_M_rN should be the files corresponding to randomly splitting the dataset to get the initial classification references, right? But somehow they are either not created or deleted at some point before the refinement actually begins.

If working with only one reference it runs normally.

Thanks in advance for helping with this issue.

niko Wed, 2015-10-28 20:42

Yes, the original file par and mrc files get renames and new file are generated with randomly assigned occupancies when starting classification. This should normally not be a problem unless one wants to go back and use the original files, for example if one wants to restart the classification or simply continue with one class. Renaming the old files to their original names should reset the project to what it was before starting classification.