I'm having issues with denoising after importing data normally using QIIME2.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-as918jc4.log
The error is that "Error in (function (fn, fout, maxN = c(0, 0), truncQ = c(2, 2), truncLen = c(0, :
Mismatched forward and reverse sequence files: 86106， 63444."
So I return to the "demux.qzv" file,found that the problem does exist.
My import order is
time qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path mainfest.txt --output-path demux.qza --input-format PairedEndFastqManifestPhred33
My question is why this problem occurs and how can i fix it.
You have correctly diagnosed the error: some reads are missing from your files such that the number of forward and reverse reads do not match.
This is usually because the reads were pre-filtered (maybe by the sequencing core?) before they were imported using the command you mentioned. Qiime2 works best with raw data, so if you have access to the unprocessed data, that's what I would try next.
Do you still have access to the raw data directly off the sequencer?
Well, the Illumina platform always makes the same number of forward and reverse reads in the same order, inside the fastq files. If reads are missing, like they are here, I suspect some filtering has been done.