Hello! I use qiime2-2020.2 and run it by command
conda activate qiime2-2020.2
My command was:
qiime dada2 denoise-paired
–i-demultiplexed-seqs UMtutorial-demux-paired-end.qza
–o-table 111UMtable-dada2O
–o-representative-sequences UMrep-seqs-dada2O
–p-trim-left-f 27
–p-trim-left-r 28
–p-trunc-len-f 0
–p-trunc-len-r 0
–p-n-threads 4
–verbose
–o-denoising-stats UMdenoising-stats.qza
The message is:
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
See above for debug info.
I tried to fix it, but nothing had happend…
–verbose show this:
qiime dada2 denoise-paired --i-demultiplexed-seqs UMtutorial-demux-paired-end.qza --o-table 111UMtable-dada2O --o-representative-sequences 111UMrep-seqs-dada2O --p-trim-left-f 27 --p-trim-left-r 28 --p-trunc-len-f 0 --p-trunc-len-r 0 --p-n-threads 4 --verbose --o-denoising-stats 111UMdenoising-stats.qza
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 /tmp/tmpdjxu6dyq/forward /tmp/tmpdjxu6dyq/reverse /tmp/tmpdjxu6dyq/output.tsv.biom /tmp/tmpdjxu6dyq/track.tsv /tmp/tmpdjxu6dyq/filt_f /tmp/tmpdjxu6dyq/filt_r 0 0 27 28 2.0 2.0 2 consensus 1.0 4 1000000
R version 3.6.1 (2019-07-05)
Загрузка требуемого пакета: Rcpp
Ошибка: package or namespace load failed for ‘dada2’:
.onLoad не удалось в loadNamespace() для ‘RcppParallel’, подробности:
вызов: dyn.load(tbb, local = FALSE, now = TRUE)
ошибка: не могу загрузить разделяемый объект ‘/home/irinab/miniconda3/envs/qiime2-2020.2/lib/R/library/RcppParallel/lib/libtbb.so.2’:
/home/linuxbrew/.linuxbrew/lib/libstdc++.so.6: version `CXXABI_1.3.11’ not found (required by /home/irinab/miniconda3/envs/qiime2-2020.2/lib/R/library/RcppParallel/lib/libtbb.so.2)
Выполнение остановлено
Traceback (most recent call last):
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 257, in denoise_paired
run_commands([cmd])
File “/home/irinab/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 “/home/irinab/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’, ‘/tmp/tmpdjxu6dyq/forward’, ‘/tmp/tmpdjxu6dyq/reverse’, ‘/tmp/tmpdjxu6dyq/output.tsv.biom’, ‘/tmp/tmpdjxu6dyq/track.tsv’, ‘/tmp/tmpdjxu6dyq/filt_f’, ‘/tmp/tmpdjxu6dyq/filt_r’, ‘0’, ‘0’, ‘27’, ‘28’, ‘2.0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘4’, ‘1000000’]’ returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-455>”, line 2, in denoise_paired
File “/home/irinab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 245, in bound_callable
output_types, provenance)
File “/home/irinab/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 “/home/irinab/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 1), please inspect stdout and stderr to learn more.