Hi
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"),
]
run_cmd(command)
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