Hi all!
Working through some data and I keep getting errors on these files. I was originally getting return code -9, which I believe means that I’ve run out of memory (I was running QIIME2 on virtualbox through windows w/ 10GB RAM) and I’ve since set up QIIME2 through AWS, running with 68 GB RAM.
I originally ran this code:
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux-muscle.qza
–o-table table
–o-representative-sequences rep-seqs
–p-trim-left-f 34
–p-trim-left-r 6
–p-trunc-len-f 68
–p-trunc-len-r 69
and 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.
Debug info has been saved to /tmp/qiime2-q2cli-err-y9d1t8eh.log
I did some reading and thought that maybe my trimming criteria were too loose so I ran this
qiime dada2 denoise-paired
–i-demultiplexed-seqs demux-muscle.qza
–o-table table
–o-representative-sequences rep-seqs
–p-trim-left-f 34
–p-trim-left-r 19
–p-trunc-len-f 76
–p-trunc-len-r 86
–verbose
And got this return code again
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering …
- Learning Error Rates
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 179, in denoise_paired
run_commands([cmd])
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 35, in run_commands
subprocess.run(cmd, check=True)
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmphf7tbrz6/forward’, ‘/tmp/tmphf7tbrz6/reverse’, ‘/tmp/tmphf7tbrz6/output.tsv.biom’, ‘/tmp/tmphf7tbrz6/filt_f’, ‘/tmp/tmphf7tbrz6/filt_r’, ‘76’, ‘86’, ‘34’, ‘19’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status -9
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2cli/commands.py”, line 224, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 228, in bound_callable
output_types, provenance)
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 363, in callable_executor
output_views = self._callable(**view_args)
File “/home/qiime2/miniconda/envs/qiime2-2017.12/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 194, 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.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
See above for debug info.
So am I running out of memory here, or is there another problem that I’m not seeing?
Thanks again for all your help!
Leah