Hello all,
I am currently running shotgun metagenomics in Qiime2 and am going through the DADA2 step. I am using Ubuntu on a Windows PC. DADA2 was denoising samples for almost two weeks (50 large samples) until the following message occurred. I’m not quite sure what caused it and can’t find it in the forum anywhere. Thanks in advance for any help.
(qiime2-2019.7) berlinba@RHEUM-HJJPCS2:/mnt/c/Users/berlinba/documents/sequencing/qiime_trial$ qiime dada2 denoise-single --i-demultiplexed-seqs AS_qiime.qza --p-trim-left 0 --p-trunc-len 148 --p-n-threads 0 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.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_single.R /tmp/qiime2-archive-27mmzxl9/534c1dab-31b4-4b97-b720-10e6bd213e5f/data /tmp/tmpfj1kazyu/output.tsv.biom /tmp/tmpfj1kazyu/track.tsv /tmp/tmpfj1kazyu 148 0 2.0 2 Inf consensus 1.0 0 1000000 NULL 16
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.3
- Filtering …
- Learning Error Rates
449725676 total bases in 3038687 reads from 1 samples will be used for learning the error rates. - Denoise samples …
…
…
*** caught segfault ***
address 0x7f7ab5462000, cause ‘invalid permissions’
Traceback:
1: dada_uniques(names(derep[[i]]$uniques), unname(derep[[i]]$uniques), names(derep[[i]]$uniques) %in% c(priors, pseudo_priors), err, qi, opts[[“MATCH”]], opts[[“MISMATCH”]], opts[[“GAP_PENALTY”]], opts[[“USE_KMERS”]], opts[[“KDIST_CUTOFF”]], opts[[“BAND_SIZE”]], opts[[“OMEGA_A”]], opts[[“OMEGA_P”]], opts[[“OMEGA_C”]], 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”]], opts[[“GAPLESS”]], opts[[“GREEDY”]])
2: dada(drp, err = err, multithread = multithread, HOMOPOLYMER_GAP_PENALTY = HOMOPOLYMER_GAP_PENALTY, BAND_SIZE = BAND_SIZE, verbose = FALSE)
An irrecoverable exception occurred. R is aborting now …
Traceback (most recent call last):
File “/home/berlinba/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 154, in _denoise_single
run_commands([cmd])
File “/home/berlinba/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/berlinba/anaconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_single.R’, ‘/tmp/qiime2-archive-27mmzxl9/534c1dab-31b4-4b97-b720-10e6bd213e5f/data’, ‘/tmp/tmpfj1kazyu/output.tsv.biom’, ‘/tmp/tmpfj1kazyu/track.tsv’, ‘/tmp/tmpfj1kazyu’, ‘148’, ‘0’, ‘2.0’, ‘2’, ‘Inf’, ‘consensus’, ‘1.0’, ‘0’, ‘1000000’, ‘NULL’, ‘16’]’ died with <Signals.SIGSEGV: 11>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/berlinba/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/berlinba/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-457>”, line 2, in denoise_single
File “/home/berlinba/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/berlinba/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/berlinba/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 189, in denoise_single
band_size=‘16’)
File “/home/berlinba/anaconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 165, 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.
See above for debug info.