Invalid character 'a' (does not match IUPAC characters for this sequence type). Allowed characters are ACGTRYKMSWBDHVN.

[Bertram_Ji]

Hi all, when I'm using qiime2 to import my fasta file (16srRNA). The code is:

qiime tools import
--type 'FeatureData[Sequence]'
--input-path PIDwholefract_otus97num.fasta
--output-path PIDwholefract_otus97num.qza

It said that

There was a problem importing PIDwholefract_otus97num.fasta:

PIDwholefract_otus97num.fasta is not a(n) DNAFASTAFormat file:

Invalid character 'a' at position 51 on line 4 (does not match IUPAC characters for this sequence type). Allowed characters are ACGTRYKMSWBDHVN.

And then I check my file. The file's data is:

OTU_1

TGGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCCTTGGGTTGTAAAGCTCT

TTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGG

ACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTGAAaaaGTTAGTGGTGAAATCCCAGAGCTTAA

CTCTGGAACTGCCATTAAAACTTTTCAGCTAGAGTATGATAGAGGAAAGCAGAATTTCTAGTGTAGAGGTGAAATTCGTA

GATATTAGAAAGAATACCAATTGCGAAGGCAGCTTTCTGGATCATTACTGACACTGAGGAACGAAAGCATGGGTAGCGAA

GAGG

OTU_2

CAGGGAATATTGTGCAATGAACGAAAGTTTGACACAGCGACACCGCGTGTGGGATGACGGATCTAGGTTTGTAAACCACT

TTCAGGAGGGAAGAAAATGACGGTACCTCCACAAGAAGCCCCGGCCAACTACGTGCCAGCAGCCGCGGTAATACGTAGGg

ggCGAGCGTTGTCCGGATTTATTGGGCGTAAAGAGCTCGTAGGCGGTTCAACAAGTCGGTCGTGAAAGTTCAGGGCTCAA

CCCTGAAATGTCGATCGATACTGTTGTGACTAGGATACGGTAGAGGTGAGTGGAATTCCGAGTGTAGCGGTGAAATGCGT

AGATATTCGGAGGAACACCAATTGCGAAGGCAGCTCACTGGACCGCTATCGACGCTGAGGAGCGAAAGCTAGGGGAGCAA

ACAGG

Since I just started to use it. I don't know how to refine my data. Can I just turn all the lowercase in to uppercase?

[SoilRotifer (Mike Robeson)]

Hi @Bertram_Ji ,

You can use the approach outlined here for importing and converting mixed case sequences into upper-case. That is, your command would look like:

qiime tools import \
    --input-path PIDwholefract_otus97num.fasta \
    --type 'FeatureData[Sequence]' \
    --input-format 'MixedCaseDNAFASTAFormat' \
    --output-path PIDwholefract_otus97num.qza

Give that a try and let us know how it goes.

[Bertram_Ji]

That works! Thank you so much for your help! Sorry I'm really a newbee so your answer is really helped! Have a great day!