Taxonomy files error

mothur bugs
1

Hi,

I was getting an error while using classify.seqs, indicating several sequences were present in the template file but not in the taxonomy file. I downloaded the TaxonomyFiles folder on 22/10/2014. On checking the two files, there are different number of sequences in the two files. File “silva.full.taxonomy” has 14227 sequences, while file “silva.bacteria.fasta” has 14272 sequences.

Cheers,
Ameet

2

Hi,

Another small error in the taxonomy file.

Reading in the /home/ameet/databases/silva.full.taxonomy taxonomy… AB067647.1 has an error in the taxonomy. This may be due to a ;;
AF419664.1 has an error in the taxonomy. This may be due to a ;;
AF419667.1 has an error in the taxonomy. This may be due to a ;;
AF507690.1 has an error in the taxonomy. This may be due to a ;;
AY428572.1 has an error in the taxonomy. This may be due to a ;;
AY536218.1 has an error in the taxonomy. This may be due to a ;;

Cheers,
Ameet

1 Like
3

Where are you getting these files from?

4

I used the link on the Phylotype page to download the taxonomy files. See linke below.
http://www.mothur.org/w/images/b/bf/TaxonomyFiles.zip

5

Those are example files for running the phylotype command. phylotype takes its input from running classify.seqs. To run classify seqs you need a reference taxonomy that you can get from here:

http://www.mothur.org/wiki/Taxonomy_outline

6

thanks very much!