I was trying to work through the steps of the Atacama Tutorial, and I ran into an error at the DADA2 step. I tried running that step with the files that I generated from the previous step, and then I tried it again using the file available in the tutorial. Both times it failed in seemingly identical ways (DADA return code -9, with the log seeming to indicate that “The filter removed all reads”)
This is the command from the command line (Note that demux-2.qza is the downloaded file – I didn’t want to overwrite my file):
qiime dada2 denoise-paired
This is the error:
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-x51nddpd.log
These are the contents of the error log:
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/tmpfxkmf8do/forward /tmp/tmpfxkmf8do/reverse /tmp/tmpfxkmf8do/output.tsv.biom /tmp/tmpfxkmf8do/track.tsv /tmp/tmpfxkmf8do/filt_f /tmp/tmpfxkmf8do/filt_r 150 150 13 13 2.0 2.0 2 consensus 1.0 1 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.3 / RcppParallel: 4.4.4
- Filtering The filter removed all reads: /tmp/tmpfxkmf8do/filt_f/BAQ1370.1.3_57_L001_R1_001.fastq.gz and /tmp/tmpfxkmf8do/filt_r/BAQ1370.1.3_57_L001_R2_001.fastq.gz not written.
The filter removed all reads: /tmp/tmpfxkmf8do/filt_f/BAQ1370.3_71_L001_R1_001.fastq.gz and /tmp/tmpfxkmf8do/filt_r/BAQ1370.3_71_L001_R2_001.fastq.gz not written.
Running QIIME2 2020.2 on VirtualBox.