Hello,
I am pretty new to using QIIME2. I have already imported my data via the manifests version, and I am currently trying to denoise my data using DADA2. I keep getting Return Code one, and I did to a 'qiime tools validate' on the file and everything seems to be ok. Not sure how to proceed. Also, I did run a q-score on the data as well and everything seems to be ok. My error is pasted below. Thanks!
qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux.qza
--p-trim-left-f 15
--p-trim-left-r 15
--p-trunc-len-f 225
--p-trunc-len-r 205
--p-n-threads 0
--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/tmp450ej6il/forward /tmp/tmp450ej6il/reverse /tmp/tmp450ej6il/output.tsv.biom /tmp/tmp450ej6il/track.tsv /tmp/tmp450ej6il/filt_f /tmp/tmp450ej6il/filt_r 225 205 15 15 2.0 2.0 2 consensus 1.0 0 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 Error in names(answer) <- names1 : attempt to set an attribute on NULL
Execution halted
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/tmp450ej6il/forward', '/tmp/tmp450ej6il/reverse', '/tmp/tmp450ej6il/output.tsv.biom', '/tmp/tmp450ej6il/track.tsv', '/tmp/tmp450ej6il/filt_f', '/tmp/tmp450ej6il/filt_r', '225', '205', '15', '15', '2.0', '2.0', '2', 'consensus', '1.0', '0', '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/qiime2-2019.10/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
" 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.