Hi, thanks for seeing this. I’m using qiime2-2023.2 in Linux. I run dada2 with this command:
time qiime dada2 denoise-paired
–i-demultiplexed-seqs demux.qza
–p-trim-left-f 0
–p-trim-left-r 0
–p-trunc-len-f 250
–p-trunc-len-r 250
–o-table table.qza
–o-representative-sequences rep-seqs.qza
–o-denoising-stats denoising-stats.qza
I got this error：
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
The log file：
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.R --input_directory /tmp/tmpxc98kpvi/forward --input_directory_reverse /tmp/tmpxc98kpvi/reverse --output_path /tmp/tmpxc98kpvi/output.tsv.biom --output_track /tmp/tmpxc98kpvi/track.tsv --filtered_directory /tmp/tmpxc98kpvi/
filt_f --filtered_directory_reverse /tmp/tmpxc98kpvi/filt_r --truncation_length 250 --truncation_length_reverse 250 --trim_left 0 --trim_left_reverse 0 --max_expected_errors 2.0 --max_expected_errors_reverse 2.0 --truncation_quality_score 2
--min_overlap 12 --pooling_method independent --chimera_method consensus --min_parental_fold 1.0 --allow_one_off False --num_threads 1 --learn_min_reads 1000000
Warning message:
package ‘optparse’ was built under R version 4.2.1
R version 3.6.1 (2019-07-05)
Loading required package: Rcpp
Error: package or namespace load failed for ‘dada2’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/R/library/rlang/libs/rlang.so':
/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/R/library/rlang/libs/rlang.so: undefined symbol: R_ActiveBindingFunction
8: stop(msg, call. = FALSE, domain = NA)
7: value[3L]
6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
4: 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)
})
3: library(dada2)
2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
1: suppressWarnings(library(dada2))
Traceback (most recent call last):
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 326, in denoise_paired
run_commands([cmd])
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/subprocess.py", line 516, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['run_dada.R', '--input_directory', '/tmp/tmpxc98kpvi/forward', '--input_directory_reverse', '/tmp/tmpxc98kpvi/reverse', '--output_path', '/tmp/tmpxc98kpvi/output.tsv.biom', '--output_track', '/tmp/tmp
xc98kpvi/track.tsv', '--filtered_directory', '/tmp/tmpxc98kpvi/filt_f', '--filtered_directory_reverse', '/tmp/tmpxc98kpvi/filt_r', '--truncation_length', '250', '--truncation_length_reverse', '250', '--trim_left', '0', '--trim_left_reverse',
'0', '--max_expected_errors', '2.0', '--max_expected_errors_reverse', '2.0', '--truncation_quality_score', '2', '--min_overlap', '12', '--pooling_method', 'independent', '--chimera_method', 'consensus', '--min_parental_fold', '1.0', '--allo
w_one_off', 'False', '--num_threads', '1', '--learn_min_reads', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2cli/commands.py", line 352, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 234, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/qiime2/sdk/action.py", line 381, in callable_executor
output_views = self._callable(**view_args)
File "/home/u21111510052/miniconda3/envs/qiime2-2023.2/lib/python3.8/site-packages/q2_dada2/_denoise.py", line 339, in denoise_paired
raise Exception("An error was encountered while running DADA2"
Exception: An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
I don’t know why this happened. I did some attempts and did not find a suitable solution.
Can anyone help me?
Thank you very much！