Hi @Ander,
I've looked through the files you sent me. The IDs are not identical between your FASTA file and the taxonomy file. For example, There is a sequence with the label ISSIK304-14 in your FASTA file but not in your taxonomy file. There are similar IDs in your taxonomy file such as: ISSIK304-14-1 and ISSIK304-14_2.
I am not sure how you originally obtained these data, but there is clearly a disconnect between the contents of the two files. For example there are a little over 10,000 sequences in the FASTA file, but over 26,000 entries in the taxonomy file.
The error is basically telling you that it found a sequence with the ID ISSIK304-14, but could not find a corresponding taxonomy in the taxonomy file. Have you looked through the following threads:
-Mike