I’m getting an error with exit code -11 from when trying to run denoise-paired from DADA2. I tried reinstalling Rcpp and my R version 3.3.1, but no luck. Thanks.
qiime dada2 denoise-paired --i-demultiplexed-seqs lulu_raw.qza --p-trunc-len-f 210 --p-trunc-len-r 180 --output-dir dada2_output --p-n-threads 10 --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/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/forward /var/folders/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/reverse /var/folders/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/output.tsv.biom /var/folders/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/filt_f /var/folders/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/filt_r 210 180 0 0 2.0 2 consensus 1.0 10 1000000
R version 3.3.1 (2016-06-21)
Loading required package: Rcpp
*** caught segfault ***
address 0x18, cause 'memory not mapped'
Traceback:
1: dyn.load(file, DLLpath = DLLpath, ...)
2: library.dynam(lib, package, package.lib)
3: loadNamespace(package, lib.loc)
4: doTryCatch(return(expr), name, parentenv, handler)
5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
7: tryCatch(expr, error = function(e) { call <- conditionCall(e) if (!is.null(call)) { if (identical(call[[1L]], quote(doTryCatch))) call <- sys.call(-4L) dcall <- deparse(call)[1L] prefix <- paste("Error in", dcall, ": ") LONG <- 75L msg <- conditionMessage(e) sm <- strsplit(msg, "\n")[[1L]] w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") if (is.na(w)) w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], type = "b") if (w > LONG) prefix <- paste0(prefix, "\n ") } else prefix <- "Error : " msg <- paste0(prefix, conditionMessage(e), "\n") .Internal(seterrmessage(msg[1L])) if (!silent && identical(getOption("show.error.messages"), TRUE)) { cat(msg, file = stderr()) .Internal(printDeferredWarnings()) } invisible(structure(msg, class = "try-error", condition = e))})
8: try({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps)})
9: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
10: .getRequiredPackages2(pkgInfo, quietly = quietly)
11: library(dada2)
An irrecoverable exception occurred. R is aborting now ...
Traceback (most recent call last):
File "/Users/qmuncaster/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 179, in denoise_paired
run_commands([cmd])
File "/Users/qmuncaster/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2_dada2/_denoise.py", line 35, in run_commands
subprocess.run(cmd, check=True)
File "/Users/qmuncaster/miniconda3/envs/qiime2-2017.8/lib/python3.5/subprocess.py", line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/forward', '/var/folders/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/reverse', '/var/folders/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/output.tsv.biom', '/var/folders/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/filt_f', '/var/folders/1d/p1nml9712yn2pmv5hv77q9m05pr6pk/T/tmplkigq6d2/filt_r', '210', '180', '0', '0', '2.0', '2', 'consensus', '1.0', '10', '1000000']' returned non-zero exit status -11
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/qmuncaster/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/q2cli/commands.py", line 222, in __call__
results = action(**arguments)
File "<decorator-gen-132>", line 2, in denoise_paired
File "/Users/qmuncaster/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 201, in callable_wrapper
output_types, provenance)
File "/Users/qmuncaster/miniconda3/envs/qiime2-2017.8/lib/python3.5/site-packages/qiime2/sdk/action.py", line 334, in _callable_executor_
output_views = callable(**view_args)
File "/Users/qmuncaster/miniconda3/envs/qiime2-2017.8/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.