Hello, All,
I am newbie to Qiime2 and programming, I got problem in importing reference data set its_12_11_otus.tar.gz
When I was trying to create classifier file I got the following error
Plugin error from feature-classifier:
Invalid character in sequence: b’_’.
Valid characters: [’.’, ‘H’, ‘Y’, ‘K’, ‘M’, ‘D’, ‘A’, ‘N’, ‘S’, ‘T’, ‘V’, ‘B’, ‘-’, ‘W’, ‘R’, ‘C’, ‘G’]
Note: Use lowercase
if your sequence contains lowercase characters not in the sequence’s alphabet.
I have even tried this command line tr ‘acgt’ ‘ACGT’ < 97_otus.fasta.uppercase.fa > 97_otus.fasta.uppercase.fa.qza. But still, I was getting that same error.
Command line which I used was
qiime tools import --input-path 97_otus.fasta.uppercase.fa --output-path 97_otus.fasta.uppercase.fa.qza --type FeatureData[Sequence]
qiime tools import --type ‘FeatureData[Taxonomy]’ --input-format HeaderlessTSVTaxonomyFormat --input-path 97_otu_taxonomy.txt --output-path 97_otu_taxonomy.txt.qza
qiime feature-classifier fit-classifier-naive-bayes --i-reference-reads 97_otus.fasta.uppercase.fa.qza --i-reference-taxonomy 97_otu_taxonomyf.txt.qza --o-classifier 97classifier.qza
Could anyone please give suggestions about how to rectify this error? Thanking you all in anticipation.