export paired end got 1 sample relevant of 165

i merged forward and reverse reads as paired end and i got just just one sample relevant ( there is 165 samples)
taxonomy file:
otu file:

I export the data like this:

def qiime_dada2(reads_data: ReadsData, input_path: str, left: int | tuple[int, int], right: int | tuple[int, int], threads: int = 12):

paired = reads_data.fwd and reads_data.rev

trim_range = ["--p-trim-left-f", str(left[0]), "--p-trim-left-r", str(left[1])] if paired \
    else ["--p-trim-left", str(left)]
trunc_range = ["--p-trunc-len-f", str(right[0]), "--p-trunc-len-r", str(right[1])] if paired \
    else ["--p-trunc-len", str(right)]

command = [
              "qiime", "dada2", "denoise-paired" if paired else "denoise-single",
              "--i-demultiplexed-seqs", input_path,
          ] + trim_range + trunc_range + [
              "--o-table", os.path.join(reads_data.dir_path, "qza", "dada2_table.qza"),
              "--p-n-threads", str(threads),
              "--p-chimera-method", "consensus",
              "--o-representative-sequences", os.path.join(reads_data.dir_path, "qza", "dada2_rep-seqs.qza"),
              "--o-denoising-stats", os.path.join(reads_data.dir_path, "qza", "dada2_denoising-stats.qza"),

its kind of weird, because if when i export as single end the output is fine.
what do you think the problem is?
thanks in advance

Hi @shanif3,
I am going to need more context.

Where are you running this?
What User Interface are you using?
What qiime2 version are you using?

To clarify this looks like you have one feature, not one sample. Are there supposed to be 165 features or samples?

Hi @cherman2,
thanks for answering!
I built a package in python that run the process automaticlly, so im using my terminal to run it.
I'm using q2cli version 2023.2.0 (i used qiime --version to check it)
there supposed to be 165 samples

Hi @shanif3,
Could you adapt your code to print the q2cli commands that are being run, and then share those? That will enable us to debug anything that might be happening on the QIIME 2 side.

EDIT: Also, have you review the data provenance of the artifact that you're trying to export, to ensure that everything is being run as you expect within QIIME 2?

Hi @gregcaporaso,
How do i use q2cil commands in my code?
and the data that im trying to dwonload and export is public, it's not mine

Hello @shanif3,

It looks like you're using python to template out calls to the qiime2 command line interface, is that correct? If you just want to run a command or two it would be easier to just do so directly in the shell. If you're developing more complex software, you should take a look at the python API to qiime2.


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