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error in dada2 - error rates could not be estimated #2171

@lejlapasic-ctrl

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@lejlapasic-ctrl

Rekli ste:
I have 36 samples sequenced by NovaSeq (2X250 bp) that I would like to have analyzed. This is my first time using this platform. The original reads are high quality throughout their length. The primers have been removed from the dataset, and DADA2 was run with the following command
qiime dada2 denoise-paired
--i-demultiplexed-seqs demux-paired.qza
--p-trunc-len-f 250
--p-trunc-len-r 230
--p-trim-left-f 0
--p-trim-left-r 0
--p-max-ee-f 3
--p-max-ee-r 3
--p-trunc-q 2
--p-min-overlap 12
--p-max-merge-mismatch 0
--p-trim-overhang False
--p-pooling-method pseudo
--p-chimera-method consensus
--p-allow-one-off False
--p-n-threads 4
--o-table ~/Ledeniki/dada2_results/table.qza
--o-representative-sequences ~/Ledeniki/dada2_results/rep-seqs.qza
--o-denoising-stats ~/Ledeniki/dada2_results/denoising-stats.qza
--o-base-transition-stats ~/Ledeniki/dada2_results/base-transition-stats.qza

Even if I play with the truncating length, I get the same error:

An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.

log file records the following:
3) Learning Error Rates
274763000 total bases in 1099052 reads from 10 samples will be used for learning the error rates.
252781960 total bases in 1099052 reads from 10 samples will be used for learning the error rates.
Error rates could not be estimated (this is usually because of very few reads).
Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.

Any help appreciated.

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