Hi,
first, many thanks for taking your time to have a look at it
second, it does not work (this is a fresh qiime2-2020.2 environment)
(qiime2-2020.2) Ulis-MacBook-Pro:Tovel16S uli$ qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux-trimmed.qza
--p-trunc-len-f 0
--p-trunc-len-r 0
--p-trim-left-f 220
--p-trim-left-r 200
--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_paired.R /var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/forward /var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/reverse /var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/output.tsv.biom /var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/track.tsv /var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/filt_f /var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/filt_r 0 0 220 200 2.0 2.0 2 consensus 1.0 1 1000000
R version 3.6.1 (2019-07-05)
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({ attr(package, "LibPath") <- which.lib.loc ns <- loadNamespace(package, lib.loc) env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) { P <- if (!is.null(cc <- conditionCall(e))) paste(" in", deparse(cc)[1L]) else "" msg <- gettextf("package or namespace load failed for %s%s:\n %s", sQuote(package), P, conditionMessage(e)) if (logical.return) message(paste("Error:", msg), domain = NA) else stop(msg, call. = FALSE, domain = NA)})
8: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, quietly = quietly)
9: .getRequiredPackages2(pkgInfo, quietly = quietly)
10: library(dada2)
11: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
12: suppressWarnings(library(dada2))
An irrecoverable exception occurred. R is aborting now ...
Traceback (most recent call last):
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/forward', '/var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/reverse', '/var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/output.tsv.biom', '/var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/track.tsv', '/var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/filt_f', '/var/folders/jz/41p1rmwj7gj7g_lpwwsm5vy40000gn/T/tmplv_1bund/filt_r', '0', '0', '220', '200', '2.0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' died with <Signals.SIGSEGV: 11>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-475>", line 2, in denoise_paired
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/Users/uli/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 272, 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.
Actually, I think (maybe) to know what is going on: dada2 is unable to merge my forward and reversed reads; maybe return code -11 is pointing to this. I executed dada2 in R and it is not able to merge my sequences; I do not know why because it looks fine, but evidence is against me.
many thanks for your help,
Ulrike
