xinehc / args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
MIT License
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please help me when i run args_oap stage_one -i inputfqs -o output -f fa -t 8 i got #20

Closed darwin4442 closed 9 months ago

darwin4442 commented 1 year ago

args_oap stage_one -i inputfqs -o output -f fa -t 8 [2023-04-03 09:28:49] INFO: Building databases ... Traceback (most recent call last): File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/bin/args_oap", line 33, in sys.exit(load_entry_point('args-oap==3.2.2', 'console_scripts', 'args_oap')()) File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/site-packages/args_oap-3.2.2-py3.8.egg/args_oap/args_oap.py", line 97, in main options.func(options) File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/site-packages/args_oap-3.2.2-py3.8.egg/args_oap/stage_one.py", line 204, in run_stage_one StageOne(vars(options)).run() File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/site-packages/args_oap-3.2.2-py3.8.egg/args_oap/stage_one.py", line 51, in init make_db(file) File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/site-packages/args_oap-3.2.2-py3.8.egg/args_oap/make_db.py", line 19, in make_db subp = subprocess.run(['diamond', 'makedb', '--in', file, '--db', file, '--quiet'], check=False, stderr=subprocess.PIPE) File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/subprocess.py", line 493, in run with Popen(*popenargs, *kwargs) as process: File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/subprocess.py", line 858, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/subprocess.py", line 1704, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) PermissionError: [Errno 13] Permission denied: 'diamond' (args_oap) [acqq96qj2f@login06 example]$ wget https://dl.dropboxusercontent.com/s/pqgftlo24rfc2rd/example.tar.gz --2023-04-03 09:30:08-- https://dl.dropboxusercontent.com/s/pqgftlo24rfc2rd/example.tar.gz Resolving dl.dropboxusercontent.com (dl.dropboxusercontent.com)... 168.143.171.154, 2a03:2880:f129:83:face:b00c:0:25de Connecting to dl.dropboxusercontent.com (dl.dropboxusercontent.com)|168.143.171.154|:443... failed: Connection timed out. Connecting to dl.dropboxusercontent.com (dl.dropboxusercontent.com)|2a03:2880:f129:83:face:b00c:0:25de|:443... failed: Network is unreachable. (args_oap) [acqq96qj2f@login06 example]$ args_oap stage_one -i inputfqs -o output -f fa -t 80 [2023-04-03 09:33:44] INFO: Building databases ... Traceback (most recent call last): File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/bin/args_oap", line 33, in sys.exit(load_entry_point('args-oap==3.2.2', 'console_scripts', 'args_oap')()) File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/site-packages/args_oap-3.2.2-py3.8.egg/args_oap/args_oap.py", line 97, in main options.func(options) File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/site-packages/args_oap-3.2.2-py3.8.egg/args_oap/stage_one.py", line 204, in run_stage_one StageOne(vars(options)).run() File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/site-packages/args_oap-3.2.2-py3.8.egg/args_oap/stage_one.py", line 51, in init make_db(file) File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/site-packages/args_oap-3.2.2-py3.8.egg/args_oap/make_db.py", line 19, in make_db subp = subprocess.run(['diamond', 'makedb', '--in', file, '--db', file, '--quiet'], check=False, stderr=subprocess.PIPE) File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/subprocess.py", line 493, in run with Popen(popenargs, **kwargs) as process: File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/subprocess.py", line 858, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/public/home/acqq96qj2f/miniconda3/envs/args_oap/lib/python3.8/subprocess.py", line 1704, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) PermissionError: [Errno 13] Permission denied: 'diamond'