How to get .txt output?

[Chahat Upreti]

Hello!

I am starting using Resfinder today for the first time, and I have downloaded it locally. For some reason, the output of Resfinder is just a .json file (and some tmp files) that is hard to read. I have seen elsewhere that Resfinder also provides output neatly in a txt file. May I know how that can be done? This was my command -

python3 /Volumes/bam/DRG/PK/softwares/resfinder/resfinder.py -i /Volumes/bam/DRG/PK/genome_assemblies_genome_fasta_Refseq/ncbi-genomes-2020-05-27/GCF_000007785.1_ASM778v1_genomic.fna -o /Volumes/bam/DRG/PK/results/2020-06-04/resfinder_results/ -p /Volumes/bam/DRG/PK/softwares/resfinder_db -mp /Volumes/bam/DRG/PK/softwares/ncbi-blast-2.10.0+/bin/blastn

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[Chahat Upreti]

I found the solution. It was to use -x while running the command.

Just a suggestion - it might be great if this extended output is the default behaviour, since its much easier to work with!

[Alfred Ferrer Florensa]

Hello Chahat Upreti,

I am happy you found the solution. And we will take your advice for the ResFinder 4.0

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Best,

Alfed