[BUG]RGI 6.0.8 contig mode fails on NCBI RefSeq E. coli K-12 MG1655 (GCF_000005845.2): Requested rname NC does not exist

[ymqveneto-byte]

Describe the bug
RGI 6.0.8 fails in contig mode on the official NCBI RefSeq genome GCF_000005845.2 (Escherichia coli K-12 MG1655).

The program exits with:

Requested rname NC does not exist!

This issue is reproducible.

Interestingly, another NCBI RefSeq genome (GCF_000240185.1, Klebsiella pneumoniae HS11286) runs successfully in the same environment, suggesting a genome-specific reference name parsing or mapping issue.

I also replaced the FASTA header from:

NC_000913.3

to

contig1

while keeping the sequence identical.

The error still occurs:

Requested rname contig does not exist!

This suggests that the internal rname used by RGI no longer matches the original FASTA identifier.

Input
rgi main
-i GCF_000005845.2_ASM584v2_genomic.fna
-o ecoli
-t contig
--clean
I also tested:
rgi main
-i GCF_000005845.2_ASM584v2_genomic.fna
-o ecoli
-t contig
-a DIAMOND
--clean
The same error occurs.

Input file
Official NCBI RefSeq genome:

Accession:
GCF_000005845.2

Organism:
Escherichia coli str. K-12 substr. MG1655

Downloaded using:

datasets download genome accession GCF_000005845.2
FASTA header:

NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome

Error log
ERROR 2026-06-16 14:08:21,512 :
(Base.py::results::289)

Requested rname NC does not exist!
Please check your FASTA file.
The same error occurs when using:

-a DIAMOND

CARD Version
4.0.1
Obtained by:
rgi database --version
RGI version
Resistance Gene Identifier - 6.0.8

Obtained by:

rgi main -h
Expected behavior
RGI should successfully analyze the official NCBI RefSeq genome:

GCF_000005845.2

Escherichia coli K-12 MG1655

which is one of the most widely used bacterial reference genomes.

The output files such as:

ecoli.json
ecoli.txt

should be generated without errors.
Screenshots
If applicable, add screenshots to help explain your problem.

Desktop (please complete the following information):
OS:Ubuntu 24.04 LTS

Browser:Chrome

Version:149
Additional context
Additional observations:

The original FASTA header is:

NC_000913.3

RGI reports:

Requested rname NC does not exist

which appears to truncate the original identifier.

I replaced the FASTA header:

NC_000913.3

with

contig1

while keeping the nucleotide sequence identical.

RGI then reports:

Requested rname contig does not exist

which again appears to truncate the identifier.

Another NCBI RefSeq genome:

GCF_000240185.1

with header:

NC_016845.1

runs successfully in the exact same environment.

The issue occurs with both:

BLAST (default)

and

DIAMOND

alignment modes.

Environment:

Python: Conda environment

RGI: 6.0.8

CARD: 4.0.1

OS: Ubuntu 24.04 LTS

Installation: Bioconda

Complete terminal output

cd ~/rgi_issue_test
(base) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ conda activate rgi
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ which rgi
/home/ymq/anaconda3/envs/rgi/bin/rgi
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ rgi main -h | head -20
usage: rgi main [-h] -i INPUT_SEQUENCE -o OUTPUT_FILE [-t {contig,protein}]
                [-a {DIAMOND,BLAST}] [-n THREADS] [--include_loose]
                [--include_nudge] [--local] [--clean] [--keep] [--debug]
                [--low_quality] [-d {wgs,plasmid,chromosome,NA}] [-v]
                [-g {PRODIGAL,PYRODIGAL}]

Resistance Gene Identifier - 6.0.8 - Main

options:
  -h, --help            show this help message and exit
  -i INPUT_SEQUENCE, --input_sequence INPUT_SEQUENCE
                        input file must be in either FASTA (contig and
                        protein) or gzip format! e.g myFile.fasta,
                        myFasta.fasta.gz
  -o OUTPUT_FILE, --output_file OUTPUT_FILE
                        output folder and base filename
  -t {contig,protein}, --input_type {contig,protein}
                        specify data input type (default = contig)
  -a {DIAMOND,BLAST}, --alignment_tool {DIAMOND,BLAST}
                        specify alignment tool (default = BLAST)
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ rgi database
usage: rgi database [-h] -v [--local] [--all]
rgi database: error: the following arguments are required: -v/--version
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ rgi database -V
usage: rgi database [-h] -v [--local] [--all]
rgi database: error: the following arguments are required: -v/--version
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ rgi database --version
4.0.1
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ conda deactivate
(base) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ conda activate ncbidata
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ datasets download genome accession GCF_000005845.2
New version of client (18.30.1) available at https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets.
Collecting 1 genome record [================================================] 100% 1/1
Downloading: ncbi_dataset.zip    1.38MB valid data package
Validating package files [================================================] 100% 5/5
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ unzip ncbi_dataset.zip
Archive:  ncbi_dataset.zip
  inflating: README.md               
  inflating: ncbi_dataset/data/assembly_data_report.jsonl  
  inflating: ncbi_dataset/data/GCF_000005845.2/GCF_000005845.2_ASM584v2_genomic.fna  
  inflating: ncbi_dataset/data/dataset_catalog.json  
  inflating: md5sum.txt              
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ find ncbi_dataset -name "*.fna"
ncbi_dataset/data/GCF_000005845.2/GCF_000005845.2_ASM584v2_genomic.fna
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ conda deactivate
(base) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ conda activate rgi
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ head -1 \
ncbi_dataset/data/GCF_000005845.2/GCF_000005845.2_ASM584v2_genomic.fna
>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ mkdir result
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ rgi main \
-i ncbi_dataset/data/GCF_000005845.2/GCF_000005845.2_ASM584v2_genomic.fna \
-o result/ecoli_k12 \
-t contig \
--clean
ERROR 2026-06-16 14:08:21,512 : (Base.py::results::289) : Requested rname NC does not exist! Please check your FASTA file.
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ grep "^>" \
ncbi_dataset/data/GCF_000005845.2/GCF_000005845.2_ASM584v2_genomic.fna
>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ grep "^>" ... | wc -l
grep: ...: 没有那个文件或目录
0
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ mkdir result_diamond
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ rgi main \
-i ncbi_dataset/data/GCF_000005845.2/GCF_000005845.2_ASM584v2_genomic.fna \
-o result_diamond/ecoli_k12 \
-t contig \
-a DIAMOND \
--clean
ERROR 2026-06-16 14:10:04,331 : (Base.py::results::289) : Requested rname NC does not exist! Please check your FASTA file.
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ mkdir -p ~/rgi_issue_test/header_fix

cp \
~/rgi_issue_test/ncbi_dataset/data/GCF_000005845.2/GCF_000005845.2_ASM584v2_genomic.fna \
~/rgi_issue_test/header_fix/genome_contig1.fna
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ head -1 ~/rgi_issue_test/header_fix/genome_contig1.fna
>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ sed -i '1s/.*/>contig1/' \
~/rgi_issue_test/header_fix/genome_contig1.fna
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ head -1 ~/rgi_issue_test/header_fix/genome_contig1.fna
>contig1
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ mkdir -p ~/rgi_issue_test/header_fix/result

rgi main \
-i ~/rgi_issue_test/header_fix/genome_contig1.fna \
-o ~/rgi_issue_test/header_fix/result/ecoli \
-t contig \
--clean
ERROR 2026-06-16 14:11:31,970 : (Base.py::results::289) : Requested rname contig does not exist! Please check your FASTA file.
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ conda deactivate
(base) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ conda activate ncbidata
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test$ mkdir -p ~/rgi_issue_test/kp_test
cd ~/rgi_issue_test/kp_test
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ datasets download genome accession GCF_000240185.1
New version of client (18.30.1) available at https://ftp.ncbi.nlm.nih.gov/pub/datasets/command-line/LATEST/linux-amd64/datasets.
Collecting 1 genome record [================================================] 100% 1/1
Downloading: ncbi_dataset.zip    1.68MB valid data package
Validating package files [================================================] 100% 5/5
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ unzip ncbi_dataset.zip
Archive:  ncbi_dataset.zip
  inflating: README.md               
  inflating: ncbi_dataset/data/assembly_data_report.jsonl  
  inflating: ncbi_dataset/data/GCF_000240185.1/GCF_000240185.1_ASM24018v2_genomic.fna  
  inflating: ncbi_dataset/data/dataset_catalog.json  
  inflating: md5sum.txt              
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ find ncbi_dataset -name "*.fna"
ncbi_dataset/data/GCF_000240185.1/GCF_000240185.1_ASM24018v2_genomic.fna
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ head -1 \
ncbi_dataset/data/GCF_000240185.1/*.fna
>NC_016845.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 chromosome, complete genome
(ncbidata) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ conda deactivate
conda activate rgi
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ mkdir result
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ GENOME=$(find ncbi_dataset -name "*.fna")

rgi main \
-i $GENOME \
-o result/kp \
-t contig \
--clean
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ ls result
kp.json  kp.txt
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ head -1 $GENOME
>NC_016845.1 Klebsiella pneumoniae subsp. pneumoniae HS11286 chromosome, complete genome
(rgi) ymq@ymq-ROG-Strix-G614JV-G614JV:~/rgi_issue_test/kp_test$ 

[github-actions]

This issue is being automatically closed due to lack of activity for 30 days. While the CARD team does it's best to keep up, sometimes we are unable to do so. Please re-open this issue if you still need assistance.

[yzhong005]

Facing the same issue, would be nice if the team can reopen and look into this bug! Thank you so much!

[raphenya]

@ymqveneto-byte @yzhong005 This is indeed a bug. I will fix it. Cheers.