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AuReMe / mpwt

Pathway Tools multiprocessing wrapper (for PathoLogic).
GNU Lesser General Public License v3.0
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When I use pathway tools to build models, this problem always appears: Fatal error: The search using the name of your rganism ("Caloramator Bacteria, Firmicutes, Clostridia, Clostridiales, Caloramator." strain=NIL) failed to find any Taxon class for your organism or returned ambiguous results. #86

Closed ChenCongZ closed 1 year ago

ChenCongZ commented 1 year ago

Hi @ArnaudBelcour, When I use pathway tools to build models, this problem always appears: Fatal error: The search using the name of your organism ("Caloramator Bacteria, Firmicutes, Clostridia, Clostridiales, Caloramator." strain=NIL) failed to find any Taxon class for your organism or returned ambiguous results. Please revise your organism-params.dat file to specify an NCBI Taxonomy ID or a valid domain for your organism GCA_002400085. But I read my file and it seems to correspond to the NCBI classification. Can you show me where my problem is? The compressed package contains the information when I created it. The compressed package contains the information when I created it. model.zip

ArnaudBelcour commented 1 year ago

Hi @ChenCongZ,

There is an issue in your genbank files that leads to this error. In the line below ORGANISM (containing the taxonomy associated with your organism), you have a string with taxa names separated by , whereas it should be ;.

Your input that leads to the error (for file GCA_002400085.gbk):

SOURCE      Caloramator
  ORGANISM  Caloramator
            Bacteria, Firmicutes, Clostridia, Clostridiales, Caloramator.

The correct input:

SOURCE      Caloramator
  ORGANISM  Caloramator
            Bacteria; Firmicutes; Clostridia; Clostridiales; Caloramator.

Also as you have taxon_id.tsv, you could use the --taxon-id option to directly use the taxon ID contains in these files, that should avoid this issue. But before you should remove the organism-params.dat files in your folder as they are not correct.

ChenCongZ commented 1 year ago

Hi @ArnaudBelcour, Thank you for your help. Solve this problem and close it.