Should work search for .lst file in /Users/erocha/Genomes/Genomes/LSTINF/
Actual behavior
Searches for .lst file in /Users/erocha/Genomes/Genomes/LSTINFO/ which does not exist. (it's just an issue of an extra "O")
Steps to reproduce behavior
I think the problem in Integron_Finder/integron_finder/prot_db.py (line 186)
lst_dir_path = os.path.join(gembase_path, 'LSTINFO’)
Which should be:
lst_dir_path = os.path.join(gembase_path, 'LSTINF’)
Relevant logs and/or screenshots
(Paste any relevant logs - please use code blocks (```) to format console output,
logs, and code as it's very hard to read otherwise.)
INFO : ############ Processing replicon ESCO001.D.00001.C001 (1/1) ############
Traceback (most recent call last):
File "/Users/erocha/opt/miniconda3/envs/IFv2/bin/integron_finder", line 10, in
sys.exit(main())
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/scripts/finder.py", line 595, in main
integron_res, summary = find_integron_in_one_replicon(replicon, config)
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/scripts/finder.py", line 294, in find_integron_in_one_replicon
protein_db = GembaseDB(replicon, config)
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/prot_db.py", line 134, in init
self._info = self._parse_lst()
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/prot_db.py", line 248, in _parse_lst
gembase_type = self.gembase_sniffer(lst_path)
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/prot_db.py", line 173, in gembase_sniffer
with open(lst_path) as lst_file:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/erocha/Genomes/Genomes/LSTINFO/ESCO001.D.00001.C001.lst'
bneron
commented
3 years ago
Version of Integron_Finder:
integron_finder version 2.0rc6
OS
Expected behavior
Should work search for .lst file in /Users/erocha/Genomes/Genomes/LSTINF/
Actual behavior
Searches for .lst file in /Users/erocha/Genomes/Genomes/LSTINFO/ which does not exist. (it's just an issue of an extra "O")
Steps to reproduce behavior
I think the problem in Integron_Finder/integron_finder/prot_db.py (line 186) lst_dir_path = os.path.join(gembase_path, 'LSTINFO’) Which should be: lst_dir_path = os.path.join(gembase_path, 'LSTINF’)
Relevant logs and/or screenshots
(Paste any relevant logs - please use code blocks (```) to format console output, logs, and code as it's very hard to read otherwise.)
INFO : ############ Processing replicon ESCO001.D.00001.C001 (1/1) ############
Traceback (most recent call last): File "/Users/erocha/opt/miniconda3/envs/IFv2/bin/integron_finder", line 10, in
sys.exit(main())
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/scripts/finder.py", line 595, in main
integron_res, summary = find_integron_in_one_replicon(replicon, config)
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/scripts/finder.py", line 294, in find_integron_in_one_replicon
protein_db = GembaseDB(replicon, config)
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/prot_db.py", line 134, in init
self._info = self._parse_lst()
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/prot_db.py", line 248, in _parse_lst
gembase_type = self.gembase_sniffer(lst_path)
File "/Users/erocha/opt/miniconda3/envs/IFv2/lib/python3.6/site-packages/integron_finder/prot_db.py", line 173, in gembase_sniffer
with open(lst_path) as lst_file:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/erocha/Genomes/Genomes/LSTINFO/ESCO001.D.00001.C001.lst'