PubMLST URL change breaks pubmlstget

[rpetit3]

ariba pubmlstget "Staphylococcus aureus" datasets/species-specific/staphylococcus-aureus/mlst/default/ariba'

WARNING: I tried to get the version of spades with: "/home/rpetit/miniconda3/envs/bactopia/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)"
Traceback (most recent call last):
  File "/home/rpetit/miniconda3/envs/bactopia/bin/ariba", line 312, in <module>
    args.func(args)
  File "/home/rpetit/miniconda3/envs/bactopia/lib/python3.6/site-packages/ariba/tasks/pubmlstget.py", line 11, in run
    preparer.run()
  File "/home/rpetit/miniconda3/envs/bactopia/lib/python3.6/site-packages/ariba/pubmlst_ref_preparer.py", line 85, in run
    self._load_fasta_files_and_write_clusters_file(self.mlst_download_dir)
  File "/home/rpetit/miniconda3/envs/bactopia/lib/python3.6/site-packages/ariba/pubmlst_ref_preparer.py", line 49, in _load_fasta_files_and_write_clusters_file
    raise Error('Cannot find file "' + infile + '" for gene ' + gene_name)

verbose output

Downloading "http://pubmlst.org/data/dbases.xml" and saving as "/home/rpetit/test-grounds/tmp.get_pubmlst_xmlxwc5g9c5/out.xml" ...
Downloading "https://rest.pubmlst.org/db/pubmlst_saureus_seqdef/schemes/1/profiles_csv" and saving as "datasets/species-specific/staphylococcus-aureus/mlst/default/ariba/pubmlst_download/profile.txt" ...
Downloading "https://rest.pubmlst.org/db/pubmlst_saureus_seqdef/loci/arcC/alleles_fasta" and saving as "datasets/species-specific/staphylococcus-aureus/mlst/default/ariba/pubmlst_download/alleles_fasta.tmp" ...
Downloading "https://rest.pubmlst.org/db/pubmlst_saureus_seqdef/loci/aroE/alleles_fasta" and saving as "datasets/species-specific/staphylococcus-aureus/mlst/default/ariba/pubmlst_download/alleles_fasta.tmp" ...
Downloading "https://rest.pubmlst.org/db/pubmlst_saureus_seqdef/loci/glpF/alleles_fasta" and saving as "datasets/species-specific/staphylococcus-aureus/mlst/default/ariba/pubmlst_download/alleles_fasta.tmp" ...
Downloading "https://rest.pubmlst.org/db/pubmlst_saureus_seqdef/loci/gmk/alleles_fasta" and saving as "datasets/species-specific/staphylococcus-aureus/mlst/default/ariba/pubmlst_download/alleles_fasta.tmp" ...
Downloading "https://rest.pubmlst.org/db/pubmlst_saureus_seqdef/loci/pta/alleles_fasta" and saving as "datasets/species-specific/staphylococcus-aureus/mlst/default/ariba/pubmlst_download/alleles_fasta.tmp" ...
Downloading "https://rest.pubmlst.org/db/pubmlst_saureus_seqdef/loci/tpi/alleles_fasta" and saving as "datasets/species-specific/staphylococcus-aureus/mlst/default/ariba/pubmlst_download/alleles_fasta.tmp" ...
Downloading "https://rest.pubmlst.org/db/pubmlst_saureus_seqdef/loci/yqiL/alleles_fasta" and saving as "datasets/species-specific/staphylococcus-aureus/mlst/default/ariba/pubmlst_download/alleles_fasta.tmp"

Looks like the change in API endpoint is causing all the files are being named alleles_fasta (alleles_fasta) instead of the expected loci_name.tfa (arcC.tfa).

Getting the same error for multiple species

[rpetit3]

This is fixed on the Bioconda side. You will need to update Ariba in your Conda environment.

conda update -c conda-forge -c bioconda ariba

You should see something like:

The following packages will be UPDATED:

  ariba                               2.14.5-py36hf0b53f7_1 --> 2.14.5-py36hf0b53f7_2

After update:

ariba pubmlstget "Staphylococcus aureus" test-pubs
WARNING: I tried to get the version of spades with: "/local/home/rpetit/miniconda3/envs/bactopia/bin/spades.py --version" and the output didn't match this regular expression: "SPAdes\s+v([0-9\.]+)"
WARNING: Median sequence length is 456 but arcC.548 has length 522 which is too long or short. Removing.
WARNING: Median sequence length is 456 but arcC.567 has length 516 which is too long or short. Removing.
ariba db directory prepared. You can use it like this:
ariba run test-pubs/ref_db reads_1.fq reads_2.fq output_directory

[puethe]

Solved with #305