Import folder of fna.gz files to qiime2 artifact

qiime1
import
(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!
Ehud

p.o.
The file content is etc:

3101343_3101343.A7T31.92871
TACGTAGGTGGCAAGCGTTGTCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGATGTT
3101343_3101343.A7T31.92872
TACGTAGGTGGCAAGCGTTGCCCGGATTTACTGGGCGTAAAGGGAGCGTAGGCGGATGTT

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(Nicholas Bokulich) assigned ebolyen #2
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(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?

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(Evan Bolyen) unassigned ebolyen #4
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(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

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(Nicholas Bokulich) assigned ebolyen #6
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(Evan Bolyen) #7

Hi @Ehud,

Sorry for the excessive delay on my part. Would you be able to share the first 30 records (or 60 lines) of sample1.fna.gz and upload the file from this command?

gunzip -c sample1.fna.gz | head -n 60 > example.fna

Everything you have shared so far looks like the right way of doing this, so I need to see where our validator is falling over specifically. Since it only reads the first 30 records, we should only need 60 lines to find that out.

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(Evan Bolyen) unassigned ebolyen #8
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