refine issue

[jun zhang]

Hi all,

 I’m trying to run IsoNet refine , but I hit a file-not-found error. My command is:

isonet.py refine subtomo.star --gpuID 0,1,2,3 --iterations 30 \ --noise_start_iter 10,15,20,25 --noise_level 0.05,0.1,0.15,0.2

The run starts normally, but then crashes with:

FileNotFoundError: [Errno 2] No such file or directory: 'results/Position_7_2_9_iter00.mrc'

However, in my results/ folder, the files are named like:

Position_7_2_9_iter00.76Apx_000000 (no .mrc extension, and split into many numbered chunks)

So it seems refine is expecting a tomogram volume named: results/Position_7_2_9_iter00.mrc, but my results contain only chunked cube/subtomo files. And I’m attaching both tomograms. star and subtomo. star to this email.

Does anyone know how to fix this issue? Many thanks in advance!

[YUNTAO LIU]

Hi Jun,

Do you have a dot in your file name?

There is a problem in IsoNet that does not allow you to have that.

--
You received this message because you are subscribed to the Google Groups "IsoNet" group.
To unsubscribe from this group and stop receiving emails from it, send an email to isonet+un...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/isonet/3b293073-556d-4c27-b8aa-3c1281157bddn%40googlegroups.com.

--

Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[jun zhang]

Hi Yuntao,

Yes, my initial tomogram was named Position_7_2_9.76Apx.mrc. Thank you very much for pointing this out! After renaming it to Position_7_2_9_76Apx.mrc, everything works perfectly now.

Have a wonderful Christmas holiday!

Best regards,
Jun