Plugin error from dada2

[michoug]

Dear all,
I'm using qiime version 2017.6.0 installed via conda as described in the install pages
My OS is macOS Sierra

I tried to run the tutorial available here : “Moving Pictures” tutorial — QIIME 2 2017.6.0 documentation
When I run the command :

qiime dada2 denoise-single \
  --i-demultiplexed-seqs demux.qza \
  --p-trim-left 0 \
  --p-trunc-len 120 \
  --o-representative-sequences rep-seqs-dada2.qza \
  --o-table table-dada2.qza

I get this error :

Plugin error from dada2:

Command '['run_dada_single.R',
'/var/folders/kc/5v4myfjd0c79525lmjsjtyrh9hqckl/T/qiime2-archive-
nxksanwe/39fd29b1-7775-4335-bd47-46e4931461d1/data', '/var/folders/kc/
5v4myfjd0c79525lmjsjtyrh9hqckl/T/tmphow57op1/output.tsv.biom',
'/var/folders/kc/5v4myfjd0c79525lmjsjtyrh9hqckl/T/tmphow57op1', '120',
'0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-
zero exit status -11

Debug info has been saved to /var/folders/kc/5v4myfjd0c79525lmjsjtyrh9hqckl/T/qiime2-q2cli-err-2rcdyb89.log.

The log is attached

qiime2-q2cli-err-369kxu8v.txt (3.7 KB)

[kliere (Karsten Liere)]

Same here:

Plugin error from dada2:

Command '['run_dada_single.R',
'/var/folders/bh/s0yb0lmr8xj4n700r6_lk8b00000gn/T/qiime2-archive-
iwelp3jy/dc831848-8d68-446d-a082-5bde704f99db/data', '/var/folders/bh/
s0yb0lmr8xj4n700r6_lk8b00000gn/T/tmpdk53l8hy/output.tsv.biom',
'/var/folders/bh/s0yb0lmr8xj4n700r6_lk8b00000gn/T/tmpdk53l8hy', '120',
'0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' returned non-
zero exit status -11

Debug info has been saved to qiime2-q2cli-err-x7ryapn2.log.txt (3.7 KB)
.

[ebolyen (Evan Bolyen)]

Hey @michoug and @kliere,

Do you both have R Studio installed with dada2 already? I think I’ve seen this before and it has to do with a broken precedence for loading the R libraries. If that is the case, this issue describes a workaround. Basically you can create that .Rprofile line (in your $HOME directory) and then just delete it (or comment it out) depending on whether you are using R Studio or QIIME 2. (We’re trying to figure out how to prevent this, because we know this is a terrible workaround, things should really just work better than that.)

If you aren’t using R Studio with dada2, let us know!