lizgehret
October 4, 2022, 5:59pm
3
Hi @marioncdl ,
Thanks for reaching out and providing those details!
Self-consistency loop terminated before convergence.
It looks like this is where the issue is coming from. Here are a few forum posts that discuss this issue and contain a couple of solutions that you can try:
Hello,
I have been getting the following error after the denoising step:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
I use this command:
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --o-table table --o-representative-sequences rep-seqs --p-trim-left-f 5 --p-trim-left-r 5 --p-trunc-len-f 205 --p-trunc-len-r 205
I check the error log:
cat /var/folders/py/xrlp2jks4jq1kqx3mwf99tk…
Hi, I have been running dada2 on paired-end sequences, and had it prematurely terminate. I ran it again with the verbose command and here is the output:
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
Filtering …
Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 111645 reads in 64913 unique sequences.
Sample 2 - 104707 reads in 58972 unique sequences.
Sample 3 - 117878 reads in 68120 u…
Hello Everyone,
I am running a rather large 16S data set using dada2 and the following command:
qiime dada2 denoise-paired --i-demultiplexed-seqs 16S_demux-paired-end.qza --o-table 16S_dada2_table --o-representative-sequences 16S_rep-seqs --p-trunc-len-f 250 --p-trunc-len-r 238 --verbose --p-n-threads 0 --p-n-reads-learn 2000000
I received this warning:
Warning message:
In dada(drpsF, err = NULL, selfConsist = TRUE, multithread = multithread) :
Self-consistency loop terminated before co…
Give the suggestions in these posts a try, and let us know if you're still running into any issues!
Cheers
