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kiharalab / Emap2sec

Emap2sec is a computational tool to identify protein secondary structures
GNU General Public License v3.0
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Emap2sec.py error #17

Closed kimdn closed 2 years ago

kimdn commented 2 years ago

I'm just using tutorial set (e.g. 1733.mrc).

I think that Trimmap generation and Input dataset file generation ran well.

However,

filename='../data/input_file.txt'

echo 'data/input_dataset_file' > $filename

src="/msc/tahoma/apps/emap2sec/20220620/Emap2sec/bin/Emap2sec.py"

python $src $filename --prefix tutorial

returned Screen Shot 2022-08-16 at 9 49 49 AM

This is weird since I copied all trained models properly.

Screen Shot 2022-08-16 at 10 39 44 AM

Indeed, when I added

from os.path import exists
file_exists = exists('models/emap2sec_models_exp1/emap2sec_L1_exp.ckpt-108000.meta')
print (file_exists)

at line #314, it returned True.

Can I get some advice? Thank you.

kimdn commented 2 years ago

I fixed this issue by copying checkpoint files from codeocean's emap2sec part.

wang3702 commented 2 years ago

Glad to hear that! Also please try to use codeocean of Emap2sec and Emap2sec+ and our newer version Emap2sec+: https://github.com/kiharalab/Emap2secPlus.

kimdn commented 2 years ago

https://github.com/kiharalab/Emap2secPlus

Emap2secPlus looks nice. Maybe more accurate one? Unfortunately, I can't login codeocean without academic email address.

wang3702 commented 2 years ago

If you don't have an academic account, maybe you can easily clone emap2secplus locally to run. But I do think codeocean can make it much easier for you to configure the environment.