Hello,
I installed qiime 2 2018.8 in a VirtualBox, and I haven´t been able to run dada2 without getting this legend “An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.”
I am using the following code:
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --p-trunc-len-f 0 --p-trunc-len-r 0 --p-trim-left-f 0 --p-trim-left-r 0 --p-n-threads 0 --p-n-reads-learn 999999 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza
And the complete error message is the following:
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/tmpybvky3gc/forward /tmp/tmpybvky3gc/reverse /tmp/tmpybvky3gc/output.tsv.biom /tmp/tmpybvky3gc/track.tsv /tmp/tmpybvky3gc/filt_f /tmp/tmpybvky3gc/filt_r 0 0 0 0 2.0 2 consensus 1.0 0 999999
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
- Filtering Error in filterAndTrim(unfiltsF, filtsF, unfiltsR, filtsR, truncLen = c(truncLenF, :
These are the errors (up to 5) encountered in individual cores…
Error in add(bin) :
‘Calloc’ could not allocate memory (100000000 of 1 bytes)
Error in add(bin) :
‘Calloc’ could not allocate memory (100000000 of 1 bytes)
Error in add(bin) :
‘Calloc’ could not allocate memory (100000000 of 1 bytes)
Error in add(bin) :
‘Calloc’ could not allocate memory (100000000 of 1 bytes)
Error in add(bin) :
‘Calloc’ could not allocate memory (100000000 of 1 bytes)
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/tmpybvky3gc/forward’, ‘/tmp/tmpybvky3gc/reverse’, ‘/tmp/tmpybvky3gc/output.tsv.biom’, ‘/tmp/tmpybvky3gc/track.tsv’, ‘/tmp/tmpybvky3gc/filt_f’, ‘/tmp/tmpybvky3gc/filt_r’, ‘0’, ‘0’, ‘0’, ‘0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘0’, ‘999999’]’ 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.