Qiime2 developers: THANK YOU SO MUCH for helping me through this!
I just got an error while running DADA2 on my dataset.
Output is below:
(qiime2-2017.12) dhcp-morris-2820:Rumen ErikaGanda$ ls
Rumen-sequences.qza RumenReads rumen-demux.qzv
RumenMap.tsv rumen-demux.qza
(qiime2-2017.12) dhcp-morris-2820:Rumen ErikaGanda$ qiime dada2 denoise-single \
--i-demultiplexed-seqs rumen-demux.qza
--p-trim-left 0
--p-trunc-len 270
--o-representative-sequences rumen-rep-seqs-dada2.qza
--o-table rumen-table-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 /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/qiime2-archive-q3jvvitx/a6d39a9d-42e3-4f5d-a135-8c762b4c1ae7/data /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp2p4lt4re/output.tsv.biom /var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp2p4lt4re 270 0 2.0 2 consensus 1.0 1 1000000
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering ...............................
- Learning Error Rates
Initializing error rates to maximum possible estimate.
Sample 1 - 91807 reads in 56092 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(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 "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 126, in denoise_single
run_commands([cmd])
File "/Users/ErikaGanda/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 "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/qiime2-archive-q3jvvitx/a6d39a9d-42e3-4f5d-a135-8c762b4c1ae7/data', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp2p4lt4re/output.tsv.biom', '/var/folders/sn/92jxwrcd3qn6xp_y7c5rfdkc0000gn/T/tmp2p4lt4re', '270', '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 "/Users/ErikaGanda/miniconda3/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 "/Users/ErikaGanda/miniconda3/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py", line 228, in bound_callable
output_types, provenance)
File "/Users/ErikaGanda/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 "/Users/ErikaGanda/miniconda3/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.
See above for debug info.
(qiime2-2017.12) dhcp-morris-2820:Rumen ErikaGanda$