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[BUG] RGI may return ORF IDs instead of Contig IDs #296

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stitam opened this issue Nov 20, 2024 · 0 comments
Open

[BUG] RGI may return ORF IDs instead of Contig IDs #296

stitam opened this issue Nov 20, 2024 · 0 comments
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@stitam
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stitam commented Nov 20, 2024

Hi,

Thanks for all your work on RGI. I'm unsure whether this is intentional or a bug, let's find out :)

Describe the bug
I ran RGI with a genome that was assembled onto a single contig (chromosome). The output text file has a Contig column which as I understand should contain the name of the contig. I expected that for this particular genome the column will be the same for each entry. I did see the name of the contig, but I also saw a _[0-9]+ like suffix after the contig name and this number was unique for each entry (e.g. NZ_CP091364.1_1261, NZ_CP091364.1_2356). In my example RGI found 37 resistance genes, and assigned 37 separate "contigs" to them. I think this may be wrong: what I think is happening is that the Contig column lists ORF IDs instead of Contig IDs.

Input

This is what I'm running (inside a container):

# Load databases
rgi load -i <path_to_database_directory>/card.json --local

# Run RGI
rgi main \
  --input_sequence <path_to_sequence_file> \
  --output_file <name_of_the_assembly> \
  --local \
  --clean

Input file
In this example I used GCF_022459155.1 from NCBI.

CARD Version
v3.0.0

RGI version
v6.0.3 in a container (quay.io-biocontainers-rgi-6.0.3--pyha8f3691_0)

Expected behavior
I expected the Contig column to show only "NZ_CP091364.1"

Screenshots
Screenshot from 2024-11-20 11-00-58

Desktop (please complete the following information):
Not relevant since the tool was run in a container.

@stitam stitam added the bug label Nov 20, 2024
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