Hi,
I am just getting started with Qiime2 was able to get my demultiplexed paired end data imported to an artifact. I am now trying to run through the dada2 pipeline and running it in verbose as follows
(qiime2-2018.2) jay@Workstation:~$ qiime dada2 denoise-paired --i-demultiplexed-seqs /home/jay/zack/matt_dioxin/dioxin.qza --p-trunc-len-f 295 --p-trunc-len-r 235 --p-n-threads 0 --output-dir /home/jay/zack/matt_dioxin/dada2/ --verbose
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: run_dada_paired.R /tmp/tmpt1uq1mkd/forward /tmp/tmpt1uq1mkd/reverse /tmp/tmpt1uq1mkd/output.tsv.biom /tmp/tmpt1uq1mkd/filt_f /tmp/tmpt1uq1mkd/filt_r 295 235 0 0 2.0 2 consensus 1.0 0 1000000
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 - 92831 reads in 39069 unique sequences.
Sample 2 - 92581 reads in 38028 unique sequences.
Sample 3 - 71930 reads in 30065 unique sequences.
Sample 4 - 105089 reads in 43336 unique sequences.
Sample 5 - 87661 reads in 28261 unique sequences.
Sample 6 - 60902 reads in 21726 unique sequences.
Sample 7 - 62298 reads in 29719 unique sequences.
Sample 8 - 53804 reads in 29833 unique sequences.
Sample 9 - 92147 reads in 36507 unique sequences.
Sample 10 - 74698 reads in 36155 unique sequences.
Sample 11 - 76370 reads in 33265 unique sequences.
Sample 12 - 73091 reads in 36547 unique sequences.
Sample 13 - 147930 reads in 31751 unique sequences.
selfConsist step 2
selfConsist step 3
selfConsist step 4
selfConsist step 5
selfConsist step 6
This all seems great except for I have 20 samples with forward and reverse reads so why is it only showing 13 being processed? I exported my artifact and all 20 samples (40 total fastq files) were exported so it seems they were all included on the initial import. Is there something I am missing? Do I need to restart the dada2 command or just let it finish and check the output?
Thanks,
Zack