Cannot find database

[candyyyyyyyyyyy]

I installed the latest version via git clone. And I ran arg_oap -v, args_oap stage_one -h, args-oap, stage_two -h, and the above three commands all showed that the installation was successful。

But when I run : args-oap stage_one -i input -o out -f fa -t 20 I get an error.

The error is as follows： CRITICAL: Cannot find database </ifs1/User/sunruanyang/xrw/miniconda3/envs/args_oap2/lib/python3.7/site-packages/args_oap-3.2.4-py3.7.egg/args_oap/db/sarg.fasta>. Please run first or check database (--database).

then I check the database of the error message and found that the database existed.

Hope to get your reply.

[candyyyyyyyyyyy]

Then I try to specify the location of the database, but get the same error. The code is： args-oap stage_one -i input -o out -f fa -t 20 --database /ifs1/User/sunruanyang/xrw/miniconda3/envs/args_oap2/lib/python3.7/site-packages/args_oap-3.2.4-py3.7.egg/args_oap/db/sarg.fasta

get the same error：Cannot find database </ifs1/User/sunruanyang/xrw/miniconda3/envs/args_oap2/lib/python3.7/site-packages/args_oap-3.2.4-py3.7.egg/args_oap/db/sarg.fasta>. Please run first or check database (--database).

[xinehc]

Hi,

there seems to be an installation issue. Maybe try install via conda?

P.S. I didn't manage to reproduce the issue using:

conda create -n args_oap -c bioconda -c conda-forge diamond blast bwa samtools pandas
conda activate args_oap

git clone https://github.com/xinehc/args_oap.git
cd args_oap
python setup.py install

wget https://dl.dropboxusercontent.com/s/pqgftlo24rfc2rd/example.tar.gz
tar -xvf example.tar.gz
cd example

args_oap stage_one -i input -o output -f fa -t 8

[2023-11-10 15:13:02] INFO: Building databases ...
[2023-11-10 15:13:06] INFO: Processing <input/STAS_1.fa> (1/4) ...
[2023-11-10 15:13:13] INFO: Processing <input/STAS_2.fa> (2/4) ...
[2023-11-10 15:13:16] INFO: Processing <input/SWHAS104_1.fa> (3/4) ...
[2023-11-10 15:13:19] INFO: Processing <input/SWHAS104_2.fa> (4/4) ...
[2023-11-10 15:13:22] INFO: Finished.