error in rgi tool to detect antibiotic resistance genes

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4.2 years ago

dymphan.17phd ▴ 10

I have used the "rgi" tool to screen for antibiotic resistant genes against CARD database from the sample which are protein sequences using the command line given below.

rgi main -i Documents/MG.aa.calls.clean.fa -o Documents/CARD1/rgi/arg-1 -t protein -a DIAMOND -n 4 --low_quality

I get the following error

Error: Invalid parameter count for option '--query'
ERROR 2020-01-24 14:18:56,425 : missing blast xml file(/home/dymphan/Documents/CARD1/rgi/MG.aa.calls.clean.fa.temp.blastRes.xml). Please check if input_type: 'protein' correspond with input file: '/home/dymphan/Documents/MG.aa.calls.clean.fa' or use '--low_quality' flag for short contigs to predicts partial genes.

I would like to know the cause for the above error and any changes that need to be made.

gene next-gen sequencing sequence software error • 1.2k views

ADD COMMENT • link updated 4.2 years ago by GenoMax 141k • written 4.2 years ago by dymphan.17phd ▴ 10

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You seem to be missing a blast xml file. You also have a couple other suggestions to check in the error message.

ADD REPLY • link 4.2 years ago by GenoMax 141k

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My input file has protein sequences in fasta format. how can I get a .xml file. I have also added the other options in command line.

ADD REPLY • link 4.2 years ago by dymphan.17phd ▴ 10

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