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xinehc / args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
MIT License
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error : predicted ORF based on MAG #40

Open mengqiyue opened 1 year ago

mengqiyue commented 1 year ago

I want to use binned protein sequences to predict ARG. I downloaded the SARG v3.2.1-L (version for long read annotation) and successfully built it using "args_oap make_db -i Long_subdatabase_V3.2.1/Long_subdatabase/3.SARG_v3.2_20220917_Long_subdatabase.fasta".

6936bfe72a6139aa07489be9f1ec9c0

However, I received an error while running stage_one. I only have one protein sequence file as input, with the suffix .faa. image

When I tried changing it to .fa, it still failed to run. How can I solve this problem? I'm trying to run the first stage as follows: "args_oap stage_one -i input -o output -f fa -t 8 --database Long_subdatabase_V3.2.1/Long_subdatabase/3.SARG_v3.2_20220917_Long_subdatabase.fasta" but I get the error. I would really appreciate if you could explain me what's going on here.

Thanks a lot!

xinehc commented 1 year ago

hi,

args_oap is not designed for binned contigs or ORF. You may consider using other tools like blast/diamond/minimap to align your sequences to the protein/nucleotide SARG database.