TIR-Learner error

[chywish]

Dear author,
Thank you for your great tools for us. I have some questions need for your help.

I have installed the EDTA by following scripts:

conda create -n EDTA
conda activate EDTA
mamba install -c conda-forge -c bioconda edta

But when I take the test work by following script:

perl ~/miniconda3/envs/EDTA/bin/EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice7.0.0.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --threads 10

There is a error, such as :

2025年 01月 23日 星期四 02:23:51 CST Identify TIR candidates from scratch.
Species: others
Traceback (most recent call last):
File "/public1/home/wjguo/miniconda3/envs/EDTA/share/TIR-Learner3/TIR-Learner.py", line 15, in
from bin.main import TIRLearner
File "/public1/home/wjguo/miniconda3/envs/EDTA/share/TIR-Learner3/bin/main.py", line 36, in
class TIRLearner:
File "/public1/home/wjguo/miniconda3/envs/EDTA/share/TIR-Learner3/bin/main.py", line 383, in TIRLearner
def progress_check(self, progress_or_module: int | list, step: int = None) -> bool:
TypeError: unsupported operand type(s) for |: 'type' and 'type'
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: 没有那个文件或目录 at /public1/home/wjguo/minicond
a3/envs/EDTA/share/EDTA/bin/rename_tirlearner.pl line 19.
Warning: LOC list genome.fa.mod.TIR.ext30.list is empty.

I've reinstalled it twice, but the error still comes up！

[amvarani]

Hi there,
Same problem here!

We managed the problem installing a CPU version of tensorflow. Try this:

Reinstall your EDTA environment
conda install -c conda-forge -c bioconda tensorflow-cpu==2.11 edta

It worked for us!

good luck!

[oushujun]

@lutianyu2001 Can you please help to update the TIR-Learner's recipe?

[oushujun]

Hi @chywish, please reinstall EDTA with the updated yml file. It should specify the CPU-version of pytorch.

Hi @amvarani the tensorflow has been replaced by pytorch for easier installations. If you have the tensorflow working for you, you may keep using it.

Thanks!
Shujun

[lutianyu2001]

@lutianyu2001 Can you please help to update the TIR-Learner's recipe?

Actually, TIR-Learner's recipe does not specify which version pytorch will use, conda will automatically detect which version is suitable based on your computer. However, I can force TIR-Learner to use pytorch-cpu if needed.

[lutianyu2001]

The root cause for this problem is type hint with "|" is a new syntax that only recognized after python 3.10, however we are using python 3.8 by default.

This problem has been solved in the newer release v3.0.6. Please allow several days for bioconda to reflect this new version.