qiime dada2 denoise-paired never ending = stay at remove chimera without errors

[marioncdl (Marion)]

Hello,
I'm running qiime dada2 denoise-paired for my COI sequences but the command line never end and stay blocked at 4. Remove chimera ...

qiime tools import \
--type SampleData[PairedEndSequencesWithQuality] \
--input-path demultiplexed/COI \
--output-path 1-demultiplexed-seqs-COI.qza

I run the following code. My sequences are 250 bp PE for my barcode COI of ~380 bp
I first try with p-trunc-len 215 bp, but not reads was merged...

qiime dada2 denoise-paired 
--i-demultiplexed-seqs 1-demultiplexed-seqs-COI.qza \
--p-trim-left-f 0 \
--p-trim-left-r 0 \
--p-trunc-len-f 220 \
--p-trunc-len-r 220 \
--o-table 2-table-COI.qza \
--o-representative-sequences 2-rep-seqs-COI.qza \
--o-denoising-stats 2-denoising-stats-COI.qza \
--verbose >>Summary_denoising.txt 2>&1 &

I obtain this in my summary file :

nohup: les entrées sont ignorées
R version 3.4.1 (2017-06-30) 
Le chargement a nécessité le package : Rcpp
DADA2 R package version: 1.6.0 
1) Filtering ........................................................................................................................................................................................................
2) Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 163016 reads in 109617 unique sequences.
Sample 2 - 150183 reads in 95950 unique sequences.
Sample 3 - 161882 reads in 94093 unique sequences.
Sample 4 - 280902 reads in 145410 unique sequences.
Sample 5 - 49316 reads in 32356 unique sequences.
Sample 6 - 175446 reads in 114441 unique sequences.
Sample 7 - 232744 reads in 120860 unique sequences.
   selfConsist step 2 
   selfConsist step 3 
   selfConsist step 4 
   selfConsist step 5 
   selfConsist step 6 
   selfConsist step 7 
   selfConsist step 8 
Convergence after  8  rounds.
2b) Reverse Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 163016 reads in 127674 unique sequences.
Sample 2 - 150183 reads in 114472 unique sequences.
Sample 3 - 161882 reads in 110727 unique sequences.
Sample 4 - 280902 reads in 178398 unique sequences.
Sample 5 - 49316 reads in 35936 unique sequences.
Sample 6 - 175446 reads in 130815 unique sequences.
Sample 7 - 232744 reads in 150883 unique sequences.
   selfConsist step 2 
   selfConsist step 3 
   selfConsist step 4 
   selfConsist step 5 
   selfConsist step 6 
   selfConsist step 7 
   selfConsist step 8 
   selfConsist step 9 
   selfConsist step 10 
Self-consistency loop terminated before convergence.

3) Denoise remaining samples .................................................................................................................................................................................................
The sequences being tabled vary in length.
4) Remove chimeras (method = consensus)

I also try with a server and Qiime 2020 with the same results..
Any ideas of what happening here ?
Thanks
Marion

[lizgehret]

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:

Self-consistency loop terminated before convergence.An error was encountered while running DADA2 in R (return code 1)

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…

Dada2 Error Return Code 1, Paired-End Seqs

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…

Dada2: Self-consistency loop terminated before convergence

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

[marioncdl (Marion)]

Hi,
Thank you @lizgehret for your answers !
I tried with this following code in a web server and it's worked !

qiime dada2 denoise-paired \
  --i-demultiplexed-seqs 1-demultiplexed-seqs-COI-2.qza \
  --p-trim-left-f 0 \
  --p-trim-left-r 0 \
  --p-trunc-len-f 220 \
  --p-trunc-len-r 220 \
  --p-n-threads 24 \
  --o-table 2-table-COI-2.qza \
  --o-representative-sequences 2-rep-seqs-COI-2.qza \
  --o-denoising-stats 2-denoising-stats-COI-2.qza \
  --verbose

I think its was a problem of computing time
Thanks for your time !