qiime tools export -- output-format (Options?)

[Yali]

Hi there!

I am trying to convert “rep-seqs.qza” (q2) file to “.fna” to be used in picrust2 pipeline.

First, I tried this: qiime tools export --input-path rep-seqs.qza --output-path exported-rep-seqs-table. However, by default (without using --output-format command) it is transformed into “.fasta”, which does not work for this pipeline, so I assume must be .fna.

Then, I tried something like this:

qiime tools export
–input-path rep-seqs.qza
–output-path exported-rep-seqs-table
–output-format [something].fna

AND I got this error:
TypeError: No format: rep-seqs.fna

I have tried to find the options available for “–output-format …” but I am pretty new on this and probably I missed. Might you help me, please?

Cheers,

Yali

[jwdebelius (Justine Debelius)]

Hi @Yali,

Welcome!

A fna is a fasta. So, you could re-name the file to [something].fna after you export is.

Alternatively, have you checked out the q2-PICRUSt plugin? Would that solve your problem?

Best,
Justine

[Yali]

Hi Justine,

Many thanks for taking the time to respond to my basic question.

Just after I sent the message I found I made a mistake because I had not activated picrust2 (…conda activate picrust2). So, after that picrust2 pipeline worked with this “dna-sequences.fasta” file generated by default using qiime tools export (https://github.com/picrust/picrust2/wiki/Workflow).

I already tried q2-picrust2 and it perfectly worked with the generated artifacts from qiime 2 (filtered.table.qza and rep-seqs.qza). I obtained all the files (EC_metagenome, KO_metagenome, etc). However, I could not find a way to produce the nsti index values using that pipeline (without needing someone who can help me to develop a py script, as far as I understand). So, I was looking for exporting those artifacts table.qza to .biom ( ) and rep-seqs.qza to .fna . And then run the picrust2 pipeline.

Now, this is clear to me (fna is a fasta). Glad you all are orientating us here.

All the best,

Yali

[jwdebelius (Justine Debelius)]

Hi @Yali,

If I had a dollar for every time I failed to activate my conda enviroment, I could probably buy lunch or dinner for every qiime2 mod (and a few forum users!) I’m glad you sorted it out. I didn’t realize q2-PICRUSt was missing NIST (I know PICRUSt 1 did, I didn’t realize PICRUSt 2 had gotten there, but I dont use PICRUSt so much). Good luck with your analysis!

Best,
Justine