Feature classifier using UNITE developer sequences

[rboutin (Rozlyn Boutin)]

Hi there,
I am trying to extract reads and train a classifier using the developer sequences from UNITE. I can import the developer sequences using
qiime tools import
–type FeatureData[Sequence]
–input-path developer/sh_refs_qiime_ver7_97_01.12.2017_dev.fasta
–output-path developer/unite-ver7-97-seqs-01.12.2017.qza

However, when I run
qiime feature-classifier fit-classifier-naive-bayes
–i-reference-reads developer/unite-ver7-97-seqs-01.12.2017.qza
–i-reference-taxonomy unite-ver7-97-tax-01.12.2017-developer.qza
–o-classifier 97-classifier-deblur-developer.qza

I get the error:
Plugin error from feature-classifier:

Invalid character in sequence: b’t’.
Valid characters: [’-’, ‘G’, ‘R’, ‘A’, ‘H’, ‘.’, ‘D’, ‘B’, ‘N’, ‘M’, ‘K’, ‘V’, ‘C’, ‘T’, ‘Y’, ‘W’, ‘S’]
Note: Use lowercase if your sequence contains lowercase characters not in the sequence’s alphabet.

Is there some reformatting of the developer sequences that needs to be done to be compatible with qiime? Thanks in advance!

[Nicholas_Bokulich]

Hi @rboutin,

@rboutin

Is there some reformatting of the developer sequences that needs to be done to be compatible with qiime?

Yes, we have seen this with the developer seqs before:

Plugin error: feature-classifier extract-reads

Yowza. I have never seen that one before. As I have successfully used UNITE previously (after converting lowercase -> uppercase), I suspect the problem is being introduced on your end in one of two ways: If you are converting the files by opening in a text editor and using find/replace, the text editor might be inserting special characters (e.g., special characters for line breaks or tab characters). I recommend downloading the sequences again and converting with this command: tr 'agct' 'AGC…

Ideally we will add lowercase character support in the near future but for the time being lowercase characters should be quite rare (depending on the source dataset) and there is an easy workaround.

I hope that helps!

[rboutin (Rozlyn Boutin)]

Hi Nicholas,
Thanks for the quick reply! Yes, I just tried it again after using some code I found on a previous forum topic to convert to lowercase and things seem to be working now. Thanks again!