Import folder of fna.gz files to qiime2 artifact


(Ehud) #1

Acoording to

I try this command:
<qiime tools import --input-path file.fna --output-path file.qza --type SampleData [Sequences]>
but get this Error:
There was a problem importing file.fna:
file.fna is not a(n) QIIME1DemuxFormat file

I have also more files in fna format and I wonder what should be my next step? How can I import all the ‘fna’ files?
Actually the files now in ‘fna.gz’ format but if necessary I can gunzip all of them.

Thanks a lot!

The file content is etc:


(Nicholas Bokulich) assigned ebolyen #2

(Evan Bolyen) #3

Hey @Ehud,

Your example looks correct to me so far. Unfortunately, that particular format isn’t using our newer validate API, so it can’t really explain itself as to what’s wrong.

I suspect the issue is either a duplicate read ID or a malformatted record, which I expect both come from some issue with concatenating files.

Could you expand on where file.fna comes from?

(Evan Bolyen) unassigned ebolyen #4

(Ehud) #5

Hey @ebolyen,

Thanks for your quick respond.
The file.fna come from 3 files:

  • sample1.fna.gz
  • sample2.fna.gz
  • sample3.fna.gz
    and I concentrate them together by this command:

gunzip -c sample1.fna.gz sample2.fna.gz sample3.fna.gz | cat > file.fna

(Nicholas Bokulich) assigned ebolyen #6