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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.
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 theContig
column lists ORF IDs instead of Contig IDs.Input
This is what I'm running (inside a container):
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
Desktop (please complete the following information):
Not relevant since the tool was run in a container.
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