Dear all,
I ran the following code
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 200 --p-trunc-len-r 200 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza
My demux.qzv file is
[demux-paired-end.qzv|attachment] (upload://qRmwcUzz9VSWnF7QEKI5HAFGAXG.qzv) (289.3 KB)
and I got the following error
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
Debug info has been saved to /tmp/qiime2-q2cli-err-g3q4chxu.log
The debug info is:
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/tmpxpoksy8_/forward /tmp/tmpxpoksy8_/reverse /tmp/tmpxpoksy8_/output.tsv.biom /tmp/tmpxpoksy8_/track.tsv /tmp/tmpxpoksy8_/filt_f /tmp/tmpxpoksy8_/filt_r 200 200 0 0 2.0 2.0 2 consensus 1.0 1 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '[‘run_dada_paired.R’, '/tmp/tmpxpoksy8/forward’, '/tmp/tmpxpoksy8/reverse’, ‘/tmp/tmpxpoksy8_/output.tsv.biom’, ‘/tmp/tmpxpoksy8_/track.tsv’, ‘/tmp/tmpxpoksy8_/filt_f’, ‘/tmp/tmpxpoksy8_/filt_r’, ‘200’, ‘200’, ‘0’, ‘0’, ‘2.0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ died with <Signals.SIGKILL: 9>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py”, line 328, in call
results = action(**arguments)
File “</home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-459>”, line 2, in denoise_paired
File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2019.10/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 -9), please inspect stdout and stderr to learn more.
Can someone please help
Thank you