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