Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
Hi, i am getting this error when i try to run rgi parser ...
sh rgi1.sh
/home/bvs/Neelam/annotated/faa_json/P_aeruginosa_1.faa.json
Traceback (most recent call last):
File "rgi", line 4, in
MainBase()
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 82, in init
getattr(self, args.command)()
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 140, in parser
self.parser_run(args)
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 147, in parser_run
app.Parser.api_main(args)
File "/home/bvs/Neelam/rgi/app/Parser.py", line 273, in api_main
res = make_json(m,j,args.loose,args.type, snps)
File "/home/bvs/Neelam/rgi/app/Parser.py", line 189, in make_json
ndict['Best_Hit_ARO_classes'][j[orf][hsp]['ARO_category'][key]['category_aro_class_name']].append(j[orf][hsp]['ARO_category'][key]['category_aro_name'])
KeyError: 'Antibiotic+Adjuvant'
/home/bvs/Neelam/annotated/faa_json/P_aeruginosa_12939.faa.json
Traceback (most recent call last):
File "rgi", line 4, in
MainBase()
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 82, in init
getattr(self, args.command)()
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 140, in parser
self.parser_run(args)
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 147, in parser_run
app.Parser.api_main(args)
File "/home/bvs/Neelam/rgi/app/Parser.py", line 273, in api_main
res = make_json(m,j,args.loose,args.type, snps)
File "/home/bvs/Neelam/rgi/app/Parser.py", line 189, in make_json
ndict['Best_Hit_ARO_classes'][j[orf][hsp]['ARO_category'][key]['category_aro_class_name']].append(j[orf][hsp]['ARO_category'][key]['category_aro_name'])
KeyError: 'Antibiotic+Adjuvant'
@neelam19051 The rgi parser is used to create the JSON for the RGI wheel on the website. Currently, the Antibiotic+Adjuvant categories are not added to the wheel.
Hi, i am getting this error when i try to run rgi parser ...
sh rgi1.sh /home/bvs/Neelam/annotated/faa_json/P_aeruginosa_1.faa.json Traceback (most recent call last): File "rgi", line 4, in
MainBase()
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 82, in init
getattr(self, args.command)()
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 140, in parser
self.parser_run(args)
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 147, in parser_run
app.Parser.api_main(args)
File "/home/bvs/Neelam/rgi/app/Parser.py", line 273, in api_main
res = make_json(m,j,args.loose,args.type, snps)
File "/home/bvs/Neelam/rgi/app/Parser.py", line 189, in make_json
ndict['Best_Hit_ARO_classes'][j[orf][hsp]['ARO_category'][key]['category_aro_class_name']].append(j[orf][hsp]['ARO_category'][key]['category_aro_name'])
KeyError: 'Antibiotic+Adjuvant'
/home/bvs/Neelam/annotated/faa_json/P_aeruginosa_12939.faa.json
Traceback (most recent call last):
File "rgi", line 4, in
MainBase()
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 82, in init
getattr(self, args.command)()
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 140, in parser
self.parser_run(args)
File "/home/bvs/Neelam/rgi/app/MainBase.py", line 147, in parser_run
app.Parser.api_main(args)
File "/home/bvs/Neelam/rgi/app/Parser.py", line 273, in api_main
res = make_json(m,j,args.loose,args.type, snps)
File "/home/bvs/Neelam/rgi/app/Parser.py", line 189, in make_json
ndict['Best_Hit_ARO_classes'][j[orf][hsp]['ARO_category'][key]['category_aro_class_name']].append(j[orf][hsp]['ARO_category'][key]['category_aro_name'])
KeyError: 'Antibiotic+Adjuvant'
thank you