DADA2 errors - return code 1 and 11

[thermokarst]

Hi @bmillerlab, thanks for the info. Can you run the following, after you have activated your QIIME 2 2017.12 conda environment:

$ grep -r "SSE=" $CONDA_PREFIX/lib/python3.5/site-packages/q2_dada2*

You should see something like this:

/Users/matthew/miniconda3/envs/q2dev/lib/python3.5/site-packages/q2_dada2-2018.2.0.dev0+1.g94c5f7d-py3.5.egg-info/scripts/run_dada_paired.R:ddsF <- dada(drpsF, err=NULL, selfConsist=TRUE, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1)
/Users/matthew/miniconda3/envs/q2dev/lib/python3.5/site-packages/q2_dada2-2018.2.0.dev0+1.g94c5f7d-py3.5.egg-info/scripts/run_dada_paired.R:ddsR <- dada(drpsR, err=NULL, selfConsist=TRUE, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1)
/Users/matthew/miniconda3/envs/q2dev/lib/python3.5/site-packages/q2_dada2-2018.2.0.dev0+1.g94c5f7d-py3.5.egg-info/scripts/run_dada_paired.R:    { sink("/dev/null"); ddF <- dada(drpF, err=errF, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1); sink(); }
/Users/matthew/miniconda3/envs/q2dev/lib/python3.5/site-packages/q2_dada2-2018.2.0.dev0+1.g94c5f7d-py3.5.egg-info/scripts/run_dada_paired.R:    { sink("/dev/null"); ddR <- dada(drpR, err=errR, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1); sink(); }
/Users/matthew/miniconda3/envs/q2dev/lib/python3.5/site-packages/q2_dada2-2018.2.0.dev0+1.g94c5f7d-py3.5.egg-info/scripts/run_dada_single.R:  dds[[1]] <- dada(drps[[1]], err=NULL, selfConsist=TRUE, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1)
/Users/matthew/miniconda3/envs/q2dev/lib/python3.5/site-packages/q2_dada2-2018.2.0.dev0+1.g94c5f7d-py3.5.egg-info/scripts/run_dada_single.R:  dds[1:i] <- dada(drps[1:i], err=NULL, selfConsist=TRUE, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1)
/Users/matthew/miniconda3/envs/q2dev/lib/python3.5/site-packages/q2_dada2-2018.2.0.dev0+1.g94c5f7d-py3.5.egg-info/scripts/run_dada_single.R:    { sink("/dev/null"); dds[[j]] <- dada(drp, err=err, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1); sink(); }

Please copy and paste the results here. Thanks!

[bmillerlab]

OK:

$ grep -r "SSE=" $CONDA_PREFIX/lib/python3.5/site-packages/q2_dada2*
/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2-2017.12.1-py3.5.egg-info/scripts/run_dada_paired.R:ddsF <- dada(drpsF, err=NULL, selfConsist=TRUE, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1)
/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2-2017.12.1-py3.5.egg-info/scripts/run_dada_paired.R:ddsR <- dada(drpsR, err=NULL, selfConsist=TRUE, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1)
/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2-2017.12.1-py3.5.egg-info/scripts/run_dada_paired.R: { sink("/dev/null"); ddF <- dada(drpF, err=errF, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1); sink(); }
/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2-2017.12.1-py3.5.egg-info/scripts/run_dada_paired.R: { sink("/dev/null"); ddR <- dada(drpR, err=errR, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1); sink(); }
/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2-2017.12.1-py3.5.egg-info/scripts/run_dada_single.R: dds[[1]] <- dada(drps[[1]], err=NULL, selfConsist=TRUE, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1)
/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2-2017.12.1-py3.5.egg-info/scripts/run_dada_single.R: dds[1:i] <- dada(drps[1:i], err=NULL, selfConsist=TRUE, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1)
/Users/Paige/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2-2017.12.1-py3.5.egg-info/scripts/run_dada_single.R: { sink("/dev/null"); dds[[j]] <- dada(drp, err=err, multithread=multithread, VECTORIZED_ALIGNMENT=FALSE, SSE=1); sink(); }

[thermokarst]

Thanks for the info @bmillerlab. Have you tried completely removing your installation of miniconda3 and reinstalling from scratch? That sounds like a major pain, but, the only other thing I can think of right now is that your conda installation is somehow corrupted or broken on this particular machine. You could remove the whole thing by deleting the miniconda3 folder, or, you could use conda env remove -n $NAME to remove each of your conda environments (where $NAME is an environment name), then run conda clean --all to clear out the conda cache.

Sorry I don't have a better suggestion, but there certainly seems to be something ey going on here. Keep us posted!

[bmillerlab]

Hi, Umm I did remove miniconda and started all over and all stayed the same, but in desperation I began to do more web searches. One actually led me back to the forum where this issue from Jan 17 popped up -
DADA2 error (return code -6) - and what you suggested led to me Oct 2017 -
.Rprofile and .libPaths with Dada2 exit code -11 - which somehow I never saw before - guess I just kept putting in my info with the specific error message to explicitly. I ran ebolyen's suggested command:

echo ".libPaths(.libPaths()[2])" > ~/.Rprofile

AND now qiime 2 is working with my .gza. I can't believe it was that simple! Thanks for helping me and next time I'm going to do more open ended searches on the forum. Lesson learned.