Dada2 denoise-paired running takes long time

[terren (h.w)]

Hello everyone,

I use the following command to run DADA2 in the sever . But it has been running more than 24 hours (75 samples and 2.9G) and don’t finish now. I don’t know how it is going. Hope to your reply, thanks vey much.

Firstly, I activated qiime2 remotely from my laptop and submitted the job with the command of “sbatch denoised-dada2-trimmed.sh”.
The script of denoised-dada2-trimmed.sh is as follows.
#!/bin/bash
#SBATCH -J denoise-dada2-trimmed
#SBATCH -o denoise-dada2-trimmed.log
#SBATCH -e denoise-dada2-trimmed.err
#SBATCH --partition=high
#SBATCH --mem=60000M
#SBATCH -c 24
#SBATCH -t 60:00:00

qiime dada2 denoise-paired
–i-demultiplexed-seqs trimmed-seqs.qza
–p-trunc-len-f 240
–p-trunc-len-r 185
–p-n-threads 10
–p-n-reads-learn 10000
–o-table table-dada2.qza
–o-representative-sequences rep-seqs-dada2.qza
–o-denoising-stats denoising-stats-data2.qza
–verbose

After 1 day, I opened my laptop and found the job was running. The .log file is as follows.
R version 3.5.1 (2018-07-02)
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.4

1. Filtering …
2. Learning Error Rates
   3268080 total bases in 13617 reads from 3 samples will be used for learning the error rates.
   2519145 total bases in 13617 reads from 3 samples will be used for learning the error rates.
3. Denoise remaining samples …

The .err file is as follows.
Loading required package: Rcpp
Duplicate sequences in merged output.
Duplicate sequences in merged output.
Duplicate sequences in merged output.

[thermokarst]

Hi @terren, please see the following note in the DADA2 docs on estimating runtime:

https://benjjneb.github.io/dada2/bigdata.html#how-long-does-it-take