search

arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
Other
330 stars 78 forks source link

additional .fai file produced #186

Closed Biofarmer closed 2 years ago

Biofarmer commented 2 years ago

Hi, I am running contig with rgi main function with default settings. The version is 5.2.0. There are two issues that I am confused:

  1. for a few genomes (not all), an additional .fai file is produced in the directory where the genome is located, may I ask whether this is normal, is it due the genome itself? 2.warnnings like below are produced for a few genomes, may I ask whether this is normal, and can be ignored? WARNING 2022-06-27 01:55:38,858 : partial gene in card reference: aad(6) WARNING 2022-06-27 02:37:04,779 : partial gene in card reference: OXA-140

The results seem fine with two files (rgi_card.json and rgi_card.txt) produced in the output directory.

Thanks Wang

raphenya commented 2 years ago

@Biofarmer The index file.fai are normal. They are generated to search for alternate start codons and check for partials.

The warnings are also normal, they inform the user that the reference sequence in CARD are partials. Hence the user can further investigate if they have a complete gene.

Hope that helps.

Cheers, Amos.

Biofarmer commented 2 years ago

@Biofarmer The index file.fai are normal. They are generated to search for alternate start codons and check for partials.

The warnings are also normal, they inform the user that the reference sequence in CARD are partials. Hence the user can further investigate if they have a complete gene.

Hope that helps.

Cheers, Amos.

Hi Amos, many thanks for reply. Are "aad(6)" and "OXA-140" the gene names in CARD?

Biofarmer commented 2 years ago

@Biofarmer The index file.fai are normal. They are generated to search for alternate start codons and check for partials.

The warnings are also normal, they inform the user that the reference sequence in CARD are partials. Hence the user can further investigate if they have a complete gene.

Hope that helps.

Cheers, Amos.

Hi Amos, many thanks for reply. Are "aad(6)" and "OXA-140" the gene names in CARD reference?

liuyadong2023 commented 1 year ago

@Biofarmer The index file.fai are normal. They are generated to search for alternate start codons and check for partials. The warnings are also normal, they inform the user that the reference sequence in CARD are partials. Hence the user can further investigate if they have a complete gene. Hope that helps. Cheers, Amos.

Hi Amos, many thanks for reply. Are "aad(6)" and "OXA-140" the gene names in CARD?

I hope you can check this link： https://card.mcmaster.ca/ontology/39028

Biofarmer commented 1 year ago

Hi Amos, many thanks for your reply.