qiime2 tools import FeatureData[RNASequence]

User Support
,
1

I was tryin to import SILVA_138.1_SSURef_tax_silva_full_align_trunc.fasta into qiime2 with
$qiime tools import --type 'FeatureData[RNASequence]' --input-path SILVA_138.1/SILVA_138.1_SSURef_tax_silva_full_align_trunc.fasta --output-path SILVA_138.1/silva-138.1-ssu-nr-rna-seq.qza

but it give me this error
#There was a problem importing SILVA_138.1/SILVA_138.1_SSURef_tax_silva_full_align_trunc.fasta:
#SILVA_138.1/SILVA_138.1_SSURef_tax_silva_full_align_trunc.fasta is not a(n) RNAFASTAFormat file:
#Invalid character '.' at position 0 on line 2 (does not match IUPAC characters for this sequence type). Allowed characters are ACGURYKMSWBDHVN.

I know for sure that the the SILVA_database is a RNA files bun i dont know abut the '.' character. I followed the instructions of this post Processing, filtering, and evaluating the SILVA database (and other reference sequence data) with RESCRIPt, they use a different file but i cheeked and the files only differ in the quantity of information. I tried doing it with the same file that the guide but i get the same error, i am confused because they dont give the database any other treatment before import it to qiime2.

I was thinking in replacing the '.' for "-" that are also present in the file, but i am not sure that that will solve anything.

3

This issue is that you are using the incorrect type. As you are trying to import the aligned RNA SILVA FASTA files, you'll need to use --type FeatureData[AlignedRNASequence].

Give that a try and let us know if that works. :slight_smile:
-Mike

1 Like
5

HI, sorry for the late response.

It worked, thanks!!

Where can i find a guide about all the option of --type FeatureData that can be exported??

6

You can use the following command to list all of the available types:

qiime tools list-types

or you can run the following to show importable formats:

qiime tools list-formats --importable

and the following to show exportable formats:

qiime tools list-formats --exportable
1 Like
7

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.