While I was running dada2 for paired-end data I got this error:
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(qiime2-2018.8) qiime2@qiime2core2018-8:~$ qiime dada2 denoise-paired --i-demultiplexed-seqs /media/sf_gvhd/demux-paired-end.qza --o-table /media/sf_gvhd/table.qza --o-representative-sequences /media/sf_gvhd/rep-seqs.qza --p-trim-left-f 0 --p-trim-left-r 1 --p-trunc-len-f 230 --p-trunc-len-r 200 --o-denoising-stats /media/sf_gvhd/denoising-stats.qza --p-n-threads 40 --p-n-reads-learn 200000 --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.
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
Filtering ^[[AError in names(answer) <- names1 :
‘names’ attribute [115] must be the same length as the vector [98]
Execution halted
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 229, in denoise_paired
run_commands([cmd])
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmp788pga9m/forward’, ‘/tmp/tmp788pga9m/reverse’, ‘/tmp/tmp788pga9m/output.tsv.biom’, ‘/tmp/tmp788pga9m/track.tsv’, ‘/tmp/tmp788pga9m/filt_f’, ‘/tmp/tmp788pga9m/filt_r’, ‘230’, ‘200’, ‘0’, ‘1’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘40’, ‘200000’]’ returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 362, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 244, 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.
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.
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I have no idea what the problem is here…
I tried the same command after reinstalling qiime2 but I got the same error as below…
If anyone has any idea with this error… reply me please.
Thank you in advance for your help!
(qiime2-2018.8) qiime2@qiime2core2018-8:~$ qiime dada2 denoise-paired --i-demultiplexed-seqs /media/sf_gvhd/demux-paired-end.qza --o-table /media/sf_gvhd/table.qza --o-representative-sequences /media/sf_gvhd/rep-seqs.qza --p-trim-left-f 0 --p-trim-left-r 1 --p-trunc-len-f 230 --p-trunc-len-r 200 --o-denoising-stats /media/sf_gvhd/denoising-stats.qza --p-n-threads 40 --p-n-reads-learn 200000 --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.
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
Filtering Error in names(answer) <- names1 :
‘names’ attribute [115] must be the same length as the vector [97]
Execution halted
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 229, in denoise_paired
run_commands([cmd])
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmpkfp2tjad/forward’, ‘/tmp/tmpkfp2tjad/reverse’, ‘/tmp/tmpkfp2tjad/output.tsv.biom’, ‘/tmp/tmpkfp2tjad/track.tsv’, ‘/tmp/tmpkfp2tjad/filt_f’, ‘/tmp/tmpkfp2tjad/filt_r’, ‘230’, ‘200’, ‘0’, ‘1’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘40’, ‘200000’]’ returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 231, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 362, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2018.8/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 244, 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.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
It seems to be a case of an out-of-memory error happening while trimming in a multi-threaded environment.
I would change this parameter:
To something smaller OR increase the amount of memory available to you (if that's possible).
More specifically, there's not a lot of use in setting --p-n-threads higher than the number of cores available within a node, so that number should probably be something more like 4 or 8 since it looks like you are on a virtual-machine (make sure it has enough CPU's allocated from the host machine).