Hi, I ran the following code:
qiime dada2 denoise-paired
--i-demultiplexed-seqs /media/sf_470Proj/demux-paired-end.qza
--p-trim-left-f 0
--p-trim-left-r 0
--p-trunc-len-f 0
--p-trunc-len-r 235
--o-representative-sequences /media/sf_470Proj/rep-seqs-dada2.qza
--o-table /media/sf_470Proj/feature-table.qza
--o-denoising-stats /media/sf_470Proj/denoise-stat.qza
--p-n-threads 4
And receive the following error message:
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-k4rtm_p5.log
As I tried to read the log, the following info was given:
(qiime2-2019.1) qiime2@qiime2core2019-1:~$ qiime dada2 denoise-paired --i-demultiplexed-seqs /media/sf_470Proj/demux-paired-end.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 0 --p-trunc-len-r 235 --o-representative-sequences /media/sf_470Proj/rep-seqs-dada2.qza --o-table /media/sf_470Proj/feature-table.qza --o-denoising-stats /media/sf_470Proj/denoise-stat.qza --p-n-threads 4 --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.
Command: run_dada_paired.R /tmp/tmpfudfb6_5/forward /tmp/tmpfudfb6_5/reverse /tmp/tmpfudfb6_5/output.tsv.biom /tmp/tmpfudfb6_5/track.tsv /tmp/tmpfudfb6_5/filt_f /tmp/tmpfudfb6_5/filt_r 0 235 0 0 2.0 2 consensus 1.0 4 1000000
R version 3.4.1 (2017-06-30)
Loading required package: Rcpp
DADA2 R package version: 1.6.0
1) Filtering ..................
2) Learning Error Rates
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
Not all sequences were the same length.
2a) Forward Reads
Initializing error rates to maximum possible estimate.
Error in dada_uniques(names(derep[[i]]$uniques), unname(derep[[i]]$uniques), :
Memory allocation failed.
Calls: dada -> dada_uniques -> .Call
Execution halted
Warning message:
system call failed: Cannot allocate memory
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 231, in denoise_paired
run_commands([cmd])
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpfudfb6_5/forward', '/tmp/tmpfudfb6_5/reverse', '/tmp/tmpfudfb6_5/output.tsv.biom', '/tmp/tmpfudfb6_5/track.tsv', '/tmp/tmpfudfb6_5/filt_f', '/tmp/tmpfudfb6_5/filt_r', '0', '235', '0', '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/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2cli/commands.py", line 274, in __call__
results = action(**arguments)
File "</home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/decorator.py:decorator-gen-442>", line 2, in denoise_paired
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 231, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/qiime2/sdk/action.py", line 365, in _callable_executor_
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2019.1/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 246, 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.
Can you please explain what caused this error and suggest solution to overcome it?
These are our .qza and .qzv files:
demux-paired-end.qzv (291.0 KB)
Thank you in advance!