Hi,
I have successfully demultiplexed this data however, as I started to denoise my data with dada2, I keep getting the error: A pair of paired-end files were found not to have the same number of records. I have tried restarting by repeating the demultiplex step, but I continuously get that same error with different file.
The strange thing is after reviewing my qzv file in qiime2 view, it looks normal. The numbers in the error don’t add up to anything in my view file and there is no mismatched file in the qzv or my manifest tsv. I’m not sure how to go about this error. To help with writing the code I used the gut to soil tutorial: Gut-to-soil axis tutorial 💩🌱 - Microbiome marker gene analysis with QIIME 2
Here is the the my code (demultiplex and dada2), error code, qzv file:
qiime tools import \
--type 'SampleData[PairedEndSequencesWithQuality]' \
--input-path /scratch/jmc2729/rhizometagenomics/manifest.tsv \
--output-path /scratch/jmc2729/rhizometagenomics/rhizometagenome_16S_PE_demux.qza \
--input-format PairedEndFastqManifestPhred33V2
#Summarizing demultiplexed data
qiime demux summarize \
--i-data /scratch/jmc2729/rhizometagenomics/rhizometagenome_16S_PE_demux.qza \
--o-visualization rhizometagenome_16S_PE_demux.qzv
####Denoise#####
qiime dada2 denoise-paired \
--i-demultiplexed-seqs rhizometagenome_16S_PE_demux.qza \
--p-trim-left-f 0 \
--p-trunc-len-f 300 \
--p-trim-left-r 0 \
--p-trunc-len-r 300 \
--o-representative-sequences grape-seqs.qza \
--o-table grape-seqs-table.qza \
--o-denoising-stats grape-seqs-denoising-stats.qza \
--o-base-transition-stats grape-seqs-base-transition-stats.qza
qiime dada2 denoise-paired \
--i-demultiplexed-seqs rhizometagenome_16S_PE_demux.qza \
--p-trim-left-f 0 \
--p-trunc-len-f 300 \
--p-trim-left-r 0 \
--p-trunc-len-r 290 \
--o-representative-sequences grape-seqs-290.qza \
--o-table grape-seqs-290-table.qza \
--o-denoising-stats grape-seqs-290-denoising-stats.qza \
--o-base-transition-stats grape-seqs-290-base-transition-stats.qza
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