I am seeing a similar issue, I just updated by pipeline to include the new cutadapt module. This apparently completed fine, before launching into dada2 but on Linux, I wonder if it is the same issue.
Linux ashtaroth 4.13.0-19-generic #22-Ubuntu SMP Mon Dec 4 11:58:07 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Error from snakemake:
An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-dfot2w67.log
Error in job dada2Denoise while creating output files qiime2Artifacts/dada2DenoiseRepSeqs.qza, qiime2Artifacts/dada2DenoiseTable.qza.
RuleException:
CalledProcessError in line 187 of /home/dan/data/16s_data/qiime2-2017.12/Snakefile:
Command 'qiime dada2 denoise-paired --i-demultiplexed-seqs qiime2Artifacts/trimmedPairedEndImport.qza --p-trunc-len-f 265 --p-trunc-len-r 230 --o-representative-sequences qiime2Artifacts/dada2DenoiseRepSeqs.qza --o-table qiime2Artifacts/dada2DenoiseTable.qza > logs/dada2Denoise.log' returned non-zero exit status 1.
File "/home/dan/data/16s_data/qiime2-2017.12/Snakefile", line 187, in __rule_dada2Denoise
File "/home/dan/tools/miniconda3/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Will exit after finishing currently running jobs.
Exiting because a job execution failed. Look above for error message
And the entry from /tmp/qiime2-q2cli-err-dfot2w67.log:
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
1) Filtering .........
2) Learning Error Rates
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Sample 1 - 2701 reads in 1211 unique sequences.
*** caught segfault ***
address 0x10, 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(drpsF, err = NULL, selfConsist = TRUE, multithread = multithread, VECTORIZED_ALIGNMENT = FALSE, SSE = 2)
An irrecoverable exception occurred. R is aborting now ...
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/tmput1r8inm/forward /tmp/tmput1r8inm/reverse /tmp/tmput1r8inm/output.tsv.biom /tmp/tmput1r8inm/filt_f /tmp/tmput1r8inm/filt_r 265 230 0 0 2.0 2 consensus 1.0 1 1000000
Traceback (most recent call last):
File "/home/dan/tools/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/home/dan/tools/miniconda3/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/dan/tools/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmput1r8inm/forward', '/tmp/tmput1r8inm/reverse', '/tmp/tmput1r8inm/output.tsv.biom', '/tmp/tmput1r8inm/filt_f', '/tmp/tmput1r8inm/filt_r', '265', '230', '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/dan/tools/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py", line 224, in __call__
results = action(**arguments)
File "<decorator-gen-354>", line 2, in denoise_paired
File "/home/dan/tools/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/home/dan/tools/miniconda3/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/dan/tools/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 194, in denoise_paired
" 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.