Hi,
I'm trying to run the following code but I keep getting the error that follows and I'm not sure why... any help would be appreciated! I'm using qiime version 2019.10 on VirtualBox
qiime dada2 denoise-paired \
--i-demultiplexed-seqs demux-paired-end.qza
--p-trim-left-f 13
--p-trim-left-r 13
--p-trunc-len-f 251
--p-trunc-len-r 251
--o-table table.qza
--o-representative-sequences rep-seqs.qza
--o-denoising-stats denoising-stats.qza
--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/tmp3fnjl50p/forward /tmp/tmp3fnjl50p/reverse /tmp/tmp3fnjl50p/output.tsv.biom /tmp/tmp3fnjl50p/track.tsv /tmp/tmp3fnjl50p/filt_f /tmp/tmp3fnjl50p/filt_r 251 251 13 13 2.0 2.0 2 consensus 1.0 1 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.2 / RcppParallel: 4.4.4
- Filtering Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmp3fnjl50p/forward', '/tmp/tmp3fnjl50p/reverse', '/tmp/tmp3fnjl50p/output.tsv.biom', '/tmp/tmp3fnjl50p/track.tsv', '/tmp/tmp3fnjl50p/filt_f', '/tmp/tmp3fnjl50p/filt_r', '251', '251', '13', '13', '2.0', '2.0', '2', 'consensus', '1.0', '1', '1000000']' died with <Signals.SIGKILL: 9>.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-459>", line 2, in denoise_paired
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 383, in callable_executor
output_views = self._callable(**view_args)
File "/home/qiime2/miniconda/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 272, in denoise_paired