I have 3 samples from 16S rRNA gene sequenced in Illumina. I had successfully imported and trimmed primer sequences from my data but I am stuck at the denoising step. I tried so many things as suggested in the forum but still I am getting error in this step. Please help me with this.
The command I ran is:
qiime dada2 denoise-paired
I am pasting the screenshot for the error. Please help me identify the problem in this step. I will be very grateful to you.
Welcome to the forum!
The first screenshot you provided is quite blurry and difficult to read - could you please re-run your command above and simply copy/paste the results from your terminal in your response? Thanks!
This time I ran the command I got the following without generating any output file:
(qiime2-2022.2) [[email protected] Aswini_metagenome_data]$ qiime dada2 denoise-ptiplexed-seqs trimmed_seq.qza --p-trunc-len-f 0 --p-trunc-len-r 0 --p-trunc-q 20thod pooled --p-min-fold-parent-over-abundance 2 --o-table FeatureTable.qza --o-sequences Rep_seq.qza --o-denoising-stats DADA2Stats.qza --p-n-threads 10 --verbose
Running external command line application(s). This may print messages to stdout
The command(s) being run are below. These commands cannot be manually re-run as d on temporary files that no longer exist.
Command: run_dada_paired.R /tmp/tmpin90kn13/forward /tmp/tmpin90kn13/reverse /tmutput.tsv.biom /tmp/tmpin90kn13/track.tsv /tmp/tmpin90kn13/filt_f /tmp/tmpin90kn 0 2.0 2.0 20 12 independent pooled 2 10 1000000
R version 4.1.1 (2021-08-10)
Loading required package: Rcpp
DADA2: 1.22.0 / Rcpp: 188.8.131.52 / RcppParallel: 5.1.5
- Filtering Terminated
Thanks for following up and providing those details! @thermokarst pointed out that there is a SIGTERM error in the first screenshot you provided, which typically occurs when you have exceeded your resource allocation (assuming you are running QIIME 2 on some sort of cluster or server). I would recommend reaching out to your sysadmin for assistance in job submission to make sure you are requesting enough ram from your queuing system.
Hope this helps!
Thank you @lizgehret for your help.
I will try contacting my sysadmin. Hope it solves my problem.