getref broken on CARD v1.1.8

[martinghunt]

Something changed between CARD 1.1.7 and 1.1.8. ariba getref --version 1.1.7 works.

[arpcard]

@martinghunt I just checked the CARD data version 1.1.7 and 1.1.8:

running file on broadstreet-v1.1.7.tar.gz gives:
broadstreet-v1.1.7.tar.gz: bzip2 compressed data, block size = 900k

tar -tvf broadstreet-v1.1.7.tar.gz 
drwxr-xr-x git/git           0 2017-04-12 11:31 ./
-rw-r--r-- git/git       86640 2017-04-12 11:31 ./nucleotide_fasta_rRNA_mutation_model.fasta
-rw-r--r-- git/git        7204 2017-04-12 11:31 ./nucleotide_fasta_presence_and_absence_of_protein_variant_model.fasta
-rw-r--r-- git/git       10779 2017-04-12 11:31 ./mo.json
-rw-r--r-- git/git        4059 2017-04-12 11:31 ./nucleotide_fasta_protein_knockout_model.fasta
-rw-r--r-- git/git      166525 2017-04-12 11:31 ./aro_index.csv
-rw-r--r-- git/git       76107 2017-04-12 11:31 ./protein_fasta_protein_variant_model.fasta
-rw-r--r-- git/git      539616 2017-04-12 11:31 ./aro.csv
-rw-r--r-- git/git      142481 2017-04-12 11:31 ./snps.txt
-rw-r--r-- git/git        3262 2017-04-12 11:31 ./protein_fasta_presence_and_absence_of_protein_variant_model.fasta
-rw-r--r-- git/git     8132963 2017-04-12 11:31 ./card.json
-rw-r--r-- git/git        1650 2017-04-12 11:31 ./ro.csv
-rw-r--r-- git/git        1638 2017-04-12 11:31 ./protein_fasta_protein_knockout_model.fasta
-rw-r--r-- git/git       14141 2017-04-12 11:31 ./mo.obo
-rw-r--r-- git/git       85087 2017-04-12 11:31 ./ncbi_taxomony.json
-rw-r--r-- git/git        9722 2017-04-12 11:31 ./mo.csv
-rw-r--r-- git/git     5725537 2017-04-12 11:31 ./aro.owl
-rw-r--r-- git/git     2171420 2017-04-12 11:31 ./nucleotide_fasta_protein_homolog_model.fasta
-rw-r--r-- git/git        3071 2017-04-12 11:31 ./ro.obo
-rw-r--r-- git/git        2120 2017-04-12 11:31 ./ro.json
-rw-r--r-- git/git      211919 2017-04-12 11:31 ./ncbi_taxonomy.obo
-rw-r--r-- git/git      202646 2017-04-12 11:31 ./nucleotide_fasta_protein_variant_model.fasta
-rw-r--r-- git/git      801311 2017-04-12 11:31 ./protein_fasta_protein_homolog_model.fasta
-rw-r--r-- git/git     1239484 2017-04-12 11:31 ./aro.obo
-rw-r--r-- git/git      680952 2017-04-12 11:31 ./aro.json
-rw-r--r-- git/git        2059 2017-04-12 11:31 ./CARD-Download-README.txt
-rw-r--r-- git/git      342643 2017-04-12 11:31 ./aro_categories_index.csv
-rw-r--r-- git/git       45366 2017-04-12 11:31 ./ncbi_taxomony.csv

running file on broadstreet-v1.1.8.tar.gz gives:
broadstreet-v1.1.8.tar.gz: bzip2 compressed data, block size = 900k

tar -tvf broadstreet-v1.1.8.tar.gz 
drwxr-xr-x git/git           0 2017-05-04 10:35 ./
-rw-r--r-- git/git       86640 2017-05-04 10:35 ./nucleotide_fasta_rRNA_mutation_model.fasta
-rw-r--r-- git/git        7204 2017-05-04 10:35 ./nucleotide_fasta_presence_and_absence_of_protein_variant_model.fasta
-rw-r--r-- git/git       10779 2017-05-04 10:35 ./mo.json
-rw-r--r-- git/git        4059 2017-05-04 10:35 ./nucleotide_fasta_protein_knockout_model.fasta
-rw-r--r-- git/git      167000 2017-05-04 10:35 ./aro_index.csv
-rw-r--r-- git/git       76107 2017-05-04 10:35 ./protein_fasta_protein_variant_model.fasta
-rw-r--r-- git/git      541145 2017-05-04 10:35 ./aro.csv
-rw-r--r-- git/git      142565 2017-05-04 10:35 ./snps.txt
-rw-r--r-- git/git        3262 2017-05-04 10:35 ./protein_fasta_presence_and_absence_of_protein_variant_model.fasta
-rw-r--r-- git/git     8178921 2017-05-04 10:35 ./card.json
-rw-r--r-- git/git        1801 2017-05-04 10:35 ./ro.csv
-rw-r--r-- git/git        1638 2017-05-04 10:35 ./protein_fasta_protein_knockout_model.fasta
-rw-r--r-- git/git       13564 2017-05-04 10:35 ./mo.obo
-rw-r--r-- git/git       85456 2017-05-04 10:35 ./ncbi_taxomony.json
-rw-r--r-- git/git        9722 2017-05-04 10:35 ./mo.csv
-rw-r--r-- git/git     5710443 2017-05-04 10:35 ./aro.owl
-rw-r--r-- git/git     2178281 2017-05-04 10:35 ./nucleotide_fasta_protein_homolog_model.fasta
-rw-r--r-- git/git        3257 2017-05-04 10:35 ./ro.obo
-rw-r--r-- git/git        2269 2017-05-04 10:35 ./ro.json
-rw-r--r-- git/git      212669 2017-05-04 10:35 ./ncbi_taxonomy.obo
-rw-r--r-- git/git      202646 2017-05-04 10:35 ./nucleotide_fasta_protein_variant_model.fasta
-rw-r--r-- git/git      803959 2017-05-04 10:35 ./protein_fasta_protein_homolog_model.fasta
-rw-r--r-- git/git     1227157 2017-05-04 10:35 ./aro.obo
-rw-r--r-- git/git      682831 2017-05-04 10:35 ./aro.json
-rw-r--r-- git/git        2059 2017-05-04 10:35 ./CARD-Download-README.txt
-rw-r--r-- git/git      343808 2017-05-04 10:35 ./aro_categories_index.csv
-rw-r--r-- git/git       45583 2017-05-04 10:35 ./ncbi_taxomony.csv

The downloads files looks ok. The only change added was one of the keys in the card.json file was renamed.

Cheers.

Amos.

[martinghunt]

Thanks! Will fix soon. That tallies with the errors ariba is throwing.

[martinghunt]

Fixed. Reason was protein key 'GI' changed to 'accession'. New release works for all versions of CARD.