ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
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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
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darwin4442 closed 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'