Since updating to the latest QIIME2 version (qiime2-2019.10) I am struggling to get the dada2 denoise-paired command to work. I am working on a MacBook Pro using the terminal.
I have successfully imported the data as follows:
qiime tools import
qiime demux summarize
I would then like to run dada2 using the following command:
qiime dada2 denoise-paired
However I get the following error Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Debug info has been saved to /var/folders/9k/26yxjlk145v677tk0h8mm_x40000gn/T/qiime2-q2cli-err-pvaeq44u.log
The error is the following:
Command: run_dada_paired.R /var/folders/9k/26yxjlk145v677tk0h8mm_x40000gn/T/tmpx2ssgs5a/forward /var/folders/9k/26yxjlk145v677tk0h8mm_x40000gn/T/tmpx2ssgs5a/reverse /var/folders/9k/26yxjlk145v677tk0h8mm_x40000gn/T/tmpx2ssgs5a/output.tsv.biom /var/folders/9k/26yxjlk145v677tk0h8mm_x40000gn/T/tmpx2ssgs5a/track.tsv /var/folders/9k/26yxjlk145v677tk0h8mm_x40000gn/T/tmpx2ssgs5a/filt_f /var/folders/9k/26yxjlk145v677tk0h8mm_x40000gn/T/tmpx2ssgs5a/filt_r 150 150 13 13 2.0 2.0 2 consensus 1.0 0 10000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
there is no package called ‘GenomeInfoDbData’
Can someone please help me fix this? Is there a quick way of installing these packages? I didn’t get these errors when using the previous version (qiime2-2018.2).
Thank you in advance for your help and time.