Hello, I am running qiime2 2024.10 version. I am running this command for DADA2 de-noising, every time I am getting this error. qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --p-trunc-len-f 230 --p-trunc-len-r 230 --p-n-threads 4 --p-n-reads-learn 1000 --o-table table.qza…

Hello Adyasha, Here are the docs for the plugin you are running: https://docs.qiime2.org/2024.10/plugins/available/dada2/denoise-paired/ Here is the core of the error: [image] Adyasha_Panda: 375360 total bases in 1632 reads from 1 samples will be used for learning the error rates. Error rat…

Hello , No for this I'm using illumina 18S amplicon data . It's a public dataset. Project ID : PRJNA936461 I am trying to replicate the study using qiime2 pipeline. Thank you.

Okay! Then the issue is likely due to the number of reads for training: [image] Adyasha_Panda: --p-n-reads-learn 1000 Try rerunning this with more reads for the learning step. I think 1 million is the default, so 1k is pretty low. Let us know how it goes!

[image] Adyasha_Panda: -p-n-reads-learn Hi, I Have tried running with more reads, but its throwing errors. [Screenshot from 2024-11-19 11-01-30] This is the summary of my demux-paired-end.qzv file [Screenshot from 2024-11-19 11-00-36]

Can you post the full error file here? I can see a few lines, but I think there will be more clues in the full file. :scroll: Thanks!

Hi, These are the fastq files that I am using -rw-r--r-- 1 adyasha adyasha 897241 Nov 19 15:05 SRR23517960_1.fastq.gz -rw-r--r-- 1 adyasha adyasha 1027907 Nov 19 15:05 SRR23517960_2.fastq.gz -rw-r--r-- 1 adyasha adyasha 666420 Nov 19 15:05 SRR23517961_1.fastq.gz -rw-r--r-- 1 adyasha ad…

[image] Adyasha_Panda: Learning Error Rates 4191000 total bases in 16764 reads from 8 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. 6: stop("E…

Hi, This is the plot [Screenshot from 2024-11-21 09-44-34]

That's the problem! Those quality scores are not typical. For comparison, check out the quality scores from the Atacama-soils tutorial https://view.qiime2.org/visualization/?src=https://docs.qiime2.org/2024.10/data/tutorials/atacama-soils/demux-subsample.qzv Has this data been preprocessed in som…

Hi, I am not sure if this data has been preprocessed. I am using this publicly available dataset : PRJNA936461 If this data has been preprocessed then how can I run it using qiime2, is there any other way to do so ? Thank you

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Plugin error from dada2 using 18S Amplicon data

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