I am getting error after upgrade into qiime2-2017.12 while running DADA2
(qiime2-2017.12) nedonoiMac:Exp5 ruby$ qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux-Exp5.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 300 --p-trunc-len-r 277 --p-n-threads 4 --o-representative-sequences rep-seqs-exp5.qza --o-table table-exp5.qza --verbose
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 /var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/forward /var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/reverse /var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/output.tsv.biom /var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/filt_f /var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/filt_r 300 277 0 0 2.0 2 consensus 1.0 4 1000000
θ΅·εζΊεδΈγ§γ - θ¦εγ‘γγ»γΌγΈ:
1: Setting LC_COLLATE failed, using "C"
2: Setting LC_TIME failed, using "C"
3: Setting LC_MESSAGES failed, using "C"
4: Setting LC_MONETARY failed, using "C"
R version 3.4.1 (2017-06-30)
θ¦ζ±γγγγγγ±γΌγΈ Rcpp γγγΌγδΈγ§γ
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 - 52540 reads in 28609 unique sequences.
*** 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(drpsF, 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 "/Users/ruby/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/Users/ruby/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/Users/ruby/miniconda2/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/forward', '/var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/reverse', '/var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/output.tsv.biom', '/var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/filt_f', '/var/folders/2w/vhr0994d7fj3zdr08mt2py200000gp/T/tmp3ctdykgv/filt_r', '300', '277', '0', '0', '2.0', '2', 'consensus', '1.0', '4', '1000000']' returned non-zero exit status -11
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/ruby/miniconda2/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 "/Users/ruby/miniconda2/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/Users/ruby/miniconda2/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 "/Users/ruby/miniconda2/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.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -11), please inspect stdout and stderr to learn more.
See above for debug info.
Before updating to release 2017.12 I have no problem denoise my data with DADA2. My data is paired end data from fastq file imported into qiime2 artifact.
I already reinstall my qiime2 and R, but doesn't solve the problem.
Thank you
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