Error while running DADA2 command?

[Soha]

*** caught segfault ***
address 0x8, cause ‘memory not mapped’

Traceback:
1: .Call("_dada2_dada_uniques", PACKAGE = “dada2”, seqs, abundances, err, quals, score, gap, use_kmers, kdist_cutoff, band_size, omegaA, max_clust, min_fold, min_hamming, min_abund, use_quals, final_consensus, vectorized_alignment, homo_gap, multithread, verbose, SSE)
2: dada_uniques(names(derep[[i]]$uniques), unname(derep[[i]]$uniques), err, qi, opts[[“SCORE_MATRIX”]], opts[[“GAP_PENALTY”]], opts[[“USE_KMERS”]], opts[[“KDIST_CUTOFF”]], opts[[“BAND_SIZE”]], opts[[“OMEGA_A”]], if (initializeErr) { 1 } else { opts[[“MAX_CLUST”]] }, opts[[“MIN_FOLD”]], opts[[“MIN_HAMMING”]], opts[[“MIN_ABUNDANCE”]], TRUE, FALSE, opts[[“VECTORIZED_ALIGNMENT”]], opts[[“HOMOPOLYMER_GAP_PENALTY”]], multithread, (verbose >= 2), opts[[“SSE”]])
3: dada(drps[1:i], err = NULL, selfConsist = TRUE, multithread = multithread, VECTORIZED_ALIGNMENT = FALSE, SSE = 2)
An irrecoverable exception occurred. R is aborting now …
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 126, in denoise_single
run_commands([cmd])
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 35, in run_commands
subprocess.run(cmd, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_single.R’, ‘/tmp/qiime2-archive-rx2i34iy/d46613bb-148c-4e30-a84a-1130b7bebbdf/data’, ‘/tmp/tmp3zoxe4lk/output.tsv.biom’, ‘/tmp/tmp3zoxe4lk’, ‘0’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status -11

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py”, line 224, in call
results = action(**arguments)
File “”, line 2, in denoise_single
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 228, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 363, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 137, in denoise_single
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.

Plugin error from dada2:

An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.

[ebolyen (Evan Bolyen)]

Hi @Soha,

It’s been a while since we’ve seen the dreaded 0x8 error. I notice you are running 2017.12 which had an early release with this issue.

Could you provide the results of qiime info? You may just need to update to the latest QIIME 2 (in fact I would recommend that in either case!)

Otherwise, do you have an RStudio installation alongside QIIME 2 (or any other installation of R)? The library paths are known to conflict with each other causing this issue as well. In that case use:

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

to correct the problem, although this will come at the cost of RStudio’s packages.