Hi all,
I’ve been running into a similar error to this thread: https://forum.qiime2.org/t/qiime2-dada2-error/6223
However, I have been monitoring my memory and it only sits at around 30% usage when it crashes. So I don’t think that’s the issue. I’m running QIIME2 in Unbuntu 18, installed QIIME using Conda, and the computer has 40 cores and 128 GB memory.
Strangely, I don’'t have the problem when running 2019.1, but the error occurs both in 2019.4 and 2019.7.
Any ideas what the problem could be?
Kind regards,
Roger
Error below:
(qiime2-2019.7) roger@7C2R252-18:~/Analysis/16S_analysis/JOMS_Batch02_201910$ ./02_denoising.sh L01
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/tmp2zq84msi/forward /tmp/tmp2zq84msi/reverse /tmp/tmp2zq84msi/output.tsv.biom /tmp/tmp2zq84msi/track.tsv /tmp/tmp2zq84msi/filt_f /tmp/tmp2zq84msi/filt_r 280 240 20 20 6.0 6.0 2 consensus 1.0 30 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.3
- Filtering Error in names(answer) <- names1 :
‘names’ attribute [122] must be the same length as the vector [118]
Execution halted
Traceback (most recent call last):
File “/home/roger/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 234, in denoise_paired
run_commands([cmd])
File “/home/roger/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/home/roger/miniconda3/envs/qiime2-2019.7/lib/python3.6/subprocess.py”, line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/tmp/tmp2zq84msi/forward’, ‘/tmp/tmp2zq84msi/reverse’, ‘/tmp/tmp2zq84msi/output.tsv.biom’, ‘/tmp/tmp2zq84msi/track.tsv’, ‘/tmp/tmp2zq84msi/filt_f’, ‘/tmp/tmp2zq84msi/filt_r’, ‘280’, ‘240’, ‘20’, ‘20’, ‘6.0’, ‘6.0’, ‘2’, ‘consensus’, ‘1.0’, ‘30’, ‘1000000’]’ returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/roger/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/roger/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-459>”, line 2, in denoise_paired
File “/home/roger/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/roger/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 383, in callable_executor
output_views = self._callable(**view_args)
File “/home/roger/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 249, 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.