25c25
< working_directory = os.getcwd()
---
> working_directory = os.getcwd()+'/'
29,31c29,35
< path = script_path+"/_db/"
< data_path = script_path+"/_data/"
< tmp = script_path+"/_tmp/"
---
> #path = script_path+"/_db/"
> #data_path = script_path+"/_data/"
> #tmp = script_path+"/_tmp/"
> 
> path = working_directory
> data_path = working_directory
> tmp = working_directory
1111c1115,1116
< 		with open(working_directory+"/"+outputFile+".json", 'w') as f:
---
> 		#with open(working_directory+"/"+outputFile+".json", 'w') as f:
> 		with open(outputFile+".json", 'w') as f:
1457c1462
< 	parser.add_argument('-cd','--clean_databases', dest="clean_databases", default="YES", help="This removes blast databases before rgi run. Options are NO or YES (default=YES for remove)")
---
> 	parser.add_argument('-cd','--clean_databases', dest="clean_databases", default="NO", help="This removes blast databases before rgi run. Options are NO or YES (default=NO)")