Hello All:
I am running running my data through DADA 2 and have gotten a error that I have never gotten before.
An error was encountered while running DADA2 in R (return code -15), please inspect stdout and stderr to learn more.
Everything was going well prior to this and I am at a loss as to what it could be.
This is the entirety of the code:
(qiime2-2021.2) bash-5.0$ qiime dada2 denoise-paired \
--i-demultiplexed-seqs NSAID-demux.qza
--p-trim-left-f 10
--p-trim-left-r 10
--p-trunc-len-f 0
--p-trunc-len-r 0
--o-table NSAIDFeatureTable[Frequency]
--o-representative-sequences NSAIDFeatureData[Sequence]
--o-denoising-stats NSAIDSampleData[DADA2Stats}
--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/tmphiiq_sgc/forward /tmp/tmphiiq_sgc/reverse /tm p/tmphiiq_sgc/output.tsv.biom /tmp/tmphiiq_sgc/track.tsv /tmp/tmphiiq_sgc/filt_f /tmp/tmphiiq_sgc/filt_r 0 0 10 10 2.0 2.0 2 independent consensus 1.0 1 1000000
R version 4.0.2 (2020-06-22)
Loading required package: Rcpp
DADA2: 1.18.0 / Rcpp: 1.0.6 / RcppParallel: 5.0.2
- Filtering ................................................................... .................................
- Learning Error Rates
252228209 total bases in 866951 reads from 100 samples will be used for learning the error rates.
Traceback (most recent call last):
File "/home/jdchc/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dad a2/_denoise.py", line 264, in denoise_paired
run_commands([cmd])
File "/home/jdchc/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dad a2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/jdchc/.conda/envs/qiime2-2021.2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmphiiq_sgc/ forward', '/tmp/tmphiiq_sgc/reverse', '/tmp/tmphiiq_sgc/output.tsv.biom', '/tmp/ tmphiiq_sgc/track.tsv', '/tmp/tmphiiq_sgc/filt_f', '/tmp/tmphiiq_sgc/filt_r', '0 ', '0', '10', '10', '2.0', '2.0', '2', 'independent', 'consensus', '1.0', '1', ' 1000000']' died with <Signals.SIGTERM: 15>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/jdchc/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2cli/ commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/home/jdchc/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2 /sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/jdchc/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/qiime2 /sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/jdchc/.conda/envs/qiime2-2021.2/lib/python3.6/site-packages/q2_dad a2/_denoise.py", line 279, in denoise_paired
" and stderr to learn more." % e.returncode)
Exception: An error was encountered while running DADA2 in R (return code -15), please inspect stdout and stderr to learn more.
Any help or insight would be greatly appreciated.
