Dear All,
I got a bunch of topics about this problem, but I don't think that mine is also a computing resource problem.
When I ran the command below,
qiime dada2 denoise-single --i-demultiplexed-seqs demux.qza --p-n-threads 32 --p-trim-left 1 --p-trunc-len 275 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza
I got an error that "An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more"
and log file said,
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.4.6 / RcppParallel: 5.0.0
- Filtering ................................................
- Learning Error Rates
288462816 total bases in 1052784 reads from 15 samples will be used for learning the error rates.
Traceback (most recent call last):
File "/home01/r798a01/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 181, in _denoise_single
run_commands([cmd])
File "/home01/r798a01/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home01/r798a01/miniconda3/envs/qiime2-2020.6/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_single.R', '/tmp/qiime2-archive-jy8942t6/d58bea33-37ad-4cc7-8409-57f1f5a517c2/data', '/tmp/tmpd1sw9pdu/output.tsv.biom', '/tmp/tmpd1sw9pdu/track.tsv', '/tmp/tmpd1sw9pdu', '275', '1', '2.0', '2', 'Inf', 'independent', 'consensus', '1.0', '24', '1000000', 'NULL', '16']' died with <Signals.SIGKILL: 9>.During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home01/r798a01/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in denoise_single
File "/home01/r798a01/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home01/r798a01/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home01/r798a01/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 218, in denoise_single
band_size='16')
File "/home01/r798a01/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 192, in _denoise_single
" 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.
Most of the answers to this topic were about core numbers or memory problems.
But, I got 48 cores and 385Gb memory. I only ran dada2 not anything else and my free memory was 275 Gb.. But I still got the same problem.
I'm trying to reduce the reads numbers for error modeling using '--p-n-reads-learn', but still got the same problem...
Is there anyone solve this problem without any computing resources?
Thanks,
Jun