arpcard / rgi

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.
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Inconsistency summary table and results in CARD-RGI #201

Closed ikher closed 1 year ago

ikher commented 1 year ago

I have recently run a CARD-RGI job in the RGI web portal. It worked fine but I find a little inconsistency among the summary table (see below) and the results table (see below too). The summary table says I have 0+6+323 hits (perfect+strict+loose). If I download the results I get 452 lines. If I count the lines in the results table shown in the HTML table I get 452 lines, too. I have tried to filter out repeated entries based on best-hit ARO and ARO, but then I get only about 280 hits… Do you know why the numbers in the summary table and the full-length table do not match exactly? My guess is that the summary table may group/merge somehow redundant hits, but I can’t see how... Thanks in advance,

Summary table: image Results table (1st page): image

raphenya commented 1 year ago

@ikher We will look into this. Cheers.

agmcarthur commented 1 year ago

@ikher, the CARD website will update shortly with more informative text:

Summary (summary counts and figures only include Loose hits of e-10 or better)

Results (all Loose hits shown)

The download files and Results table include all possible Loose hits, but the summary table and visualizers are limited to Loose of e-10 or better.

agmcarthur commented 1 year ago

Apologies for the confusion.