CARD 3.0.6 introduces white space in seq id causing fasta/metadata mismatch

[rpetit3]

ariba getref card card
Getting available CARD versions
Downloading "https://card.mcmaster.ca/download" and saving as "download.html" ... done
Found versions:
1.0.0   https://card.mcmaster.ca/download/0/broadstreet-v1.0.0.tar.bz2
1.0.1   https://card.mcmaster.ca/download/0/broadstreet-v1.0.1.tar.bz2
1.0.2   https://card.mcmaster.ca/download/0/broadstreet-v1.0.2.tar.bz2
1.0.3   https://card.mcmaster.ca/download/0/broadstreet-v1.0.3.tar.bz2
1.0.4   https://card.mcmaster.ca/download/0/broadstreet-v1.0.4.tar.bz2
1.0.5   https://card.mcmaster.ca/download/0/broadstreet-v1.0.5.tar.bz2
1.0.6   https://card.mcmaster.ca/download/0/broadstreet-v1.0.6.tar.bz2
1.0.7   https://card.mcmaster.ca/download/0/broadstreet-v1.0.7.tar.bz2
1.0.8   https://card.mcmaster.ca/download/0/broadstreet-v1.0.8.tar.bz2
1.0.9   https://card.mcmaster.ca/download/0/broadstreet-v1.0.9.tar.bz2
1.1.0   https://card.mcmaster.ca/download/0/broadstreet-v1.1.0.tar.bz2
1.1.1   https://card.mcmaster.ca/download/0/broadstreet-v1.1.1.tar.bz2
1.1.2   https://card.mcmaster.ca/download/0/broadstreet-v1.1.2.tar.bz2
1.1.3   https://card.mcmaster.ca/download/0/broadstreet-v1.1.3.tar.bz2
1.1.4   https://card.mcmaster.ca/download/0/broadstreet-v1.1.4.tar.bz2
1.1.5   https://card.mcmaster.ca/download/0/broadstreet-v1.1.5.tar.bz2
1.1.6   https://card.mcmaster.ca/download/0/broadstreet-v1.1.6.tar.bz2
1.1.7   https://card.mcmaster.ca/download/0/broadstreet-v1.1.7.tar.bz2
1.1.8   https://card.mcmaster.ca/download/0/broadstreet-v1.1.8.tar.bz2
1.1.9   https://card.mcmaster.ca/download/0/broadstreet-v1.1.9.tar.bz2
1.2.0   https://card.mcmaster.ca/download/0/broadstreet-v1.2.0.tar.bz2
1.2.1   https://card.mcmaster.ca/download/0/broadstreet-v1.2.1.tar.bz2
2.0.0   https://card.mcmaster.ca/download/0/broadstreet-v2.0.0.tar.gz
2.0.1   https://card.mcmaster.ca/download/0/broadstreet-v2.0.1.tar.gz
2.0.2   https://card.mcmaster.ca/download/0/broadstreet-v2.0.2.tar.gz
2.0.3   https://card.mcmaster.ca/download/0/broadstreet-v2.0.3.tar.gz
3.0.0   https://card.mcmaster.ca/download/0/broadstreet-v3.0.0.tar.gz
3.0.1   https://card.mcmaster.ca/download/0/broadstreet-v3.0.1.tar.gz
3.0.2   https://card.mcmaster.ca/download/0/broadstreet-v3.0.2.tar.gz
3.0.3   https://card.mcmaster.ca/download/0/broadstreet-v3.0.3.tar.gz
3.0.4   https://card.mcmaster.ca/download/0/broadstreet-v3.0.4.tar.gz
3.0.5   https://card.mcmaster.ca/download/0/broadstreet-v3.0.5.tar.gz
3.0.6   https://card.mcmaster.ca/download/0/broadstreet-v3.0.6.tar.gz
Getting version 3.0.6
Working in temporary directory /home/rpetit3/test-grounds/slurm-test/card.download
Downloading data from card: https://card.mcmaster.ca/download/0/broadstreet-v3.0.6.tar.gz
syscall: wget -O card.tar.bz2 https://card.mcmaster.ca/download/0/broadstreet-v3.0.6.tar.gz
...finished downloading
Extracted json data file ./card.json. Reading its contents...
Found 2913 records in the json file. Analysing...
Extracted data and written ARIBA input files

Finished. Final files are:
        /home/rpetit3/test-grounds/slurm-test/card.fa
        /home/rpetit3/test-grounds/slurm-test/card.tsv

You can use them with ARIBA like this:
ariba prepareref -f /home/rpetit3/test-grounds/slurm-test/card.fa -m /home/rpetit3/test-grounds/slurm-test/card.tsv output_directory

If you use this downloaded data, please cite:
"The Comprehensive Antibiotic Resistance Database", McArthur et al 2013, PMID: 23650175
and in your methods say that version 3.0.6 of the database was used


ariba prepareref -f /home/rpetit3/test-grounds/slurm-test/card.fa -m /home/rpetit3/test-grounds/slurm-test/card.tsv output_directory
Traceback (most recent call last):
  File "/home/rpetit3/miniconda3/envs/bactopia-1.2.1/bin/ariba", line 312, in <module>
    args.func(args)
  File "/home/rpetit3/miniconda3/envs/bactopia-1.2.1/lib/python3.6/site-packages/ariba/tasks/prepareref.py", line 34, in run
    preparer.run(options.outdir)
  File "/home/rpetit3/miniconda3/envs/bactopia-1.2.1/lib/python3.6/site-packages/ariba/ref_preparer.py", line 186, in run
    genetic_code=self.genetic_code,
  File "/home/rpetit3/miniconda3/envs/bactopia-1.2.1/lib/python3.6/site-packages/ariba/reference_data.py", line 34, in __init__
    self.sequences, self.metadata = ReferenceData._load_input_files_and_check_seq_names(fasta_files, metadata_tsv_files)
  File "/home/rpetit3/miniconda3/envs/bactopia-1.2.1/lib/python3.6/site-packages/ariba/reference_data.py", line 143, in _load_input_files_and_check_seq_names
    raise Error('Sequence "' + seq_name + '" found in input fasta file but not in metadata file. Cannot continue')
ariba.reference_data.Error: Sequence "AAC(6')-29b.3002584.NG_048576.1" found in input fasta file but not in metadata file. Cannot continue

I added a line to spit out whats in the metadata dict and the fasta seq_names
(~https://github.com/sanger-pathogens/ariba/blob/master/ariba/reference_data.py#L139), here's what it is returning:

METADATA    AAC(6')-29b.3002584.NG_048576.1 101-502 (+).100-502.5869       
SEQ_NAME    AAC(6')-29b.3002584.NG_048576.1 False

Which leads me back to the seq.id = seq.id.split()[0] at https://github.com/sanger-pathogens/ariba/blob/master/ariba/reference_data.py#L139

Looks like there was whitespace introduced in v3.0.6, here's the diff for the sequence.

# v3.0.6
>gb|NG_048576.1 101-502 (+)|+|100-502|ARO:3002584|AAC(6')-29b [Pseudomonas aeruginosa]

# v3.0.5
> >gb|EU118148|+|2006-2402|ARO:3002584|AAC(6')-29b [Pseudomonas aeruginosa]

Might be a typo on CARDs end, definitely looks like it considering the 101-502 (+) is repeated.

If you think I should take this up with CARD, feel free to close this issue, and I'll follow up with them.

Cheers! Thanks for all the great work you're doing!

[kpepper]

Hi @rpetit3. Thanks for the analysis on this. Looks like CARD have it in hand.

[rpetit3]

Agreed! Going to close.