Hello, I am using qiime2-2019.7 running dada2, encountered an error. However, aftering check the topics posted all, I have no idea about solving this. My command and error info are as follows:
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux.qza --p-trunc-len-f 0 --p-trunc-len-r 0 --p-n-threads 4 --o-table table-dada2.qza --o-representative-sequences rep-seqs-dada2.qza --o-denoising-stats stats-dada2.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/tmpui69c8hs/forward /tmp/tmpui69c8hs/reverse /tmp/tmpui69c8hs/output.tsv.biom /tmp/tmpui69c8hs/track.tsv /tmp/tmpui69c8hs/filt_f /tmp/tmpui69c8hs/filt_r 0 0 0 0 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: 4.4.3
- Filtering …
- Learning Error Rates
70907162 total bases in 291823 reads from 3 samples will be used for learning the error rates.
73233596 total bases in 291823 reads from 3 samples will be used for learning the error rates.
Error in err[c(1, 6, 11, 16), ] ← 1 :
incorrect number of subscripts on matrix
Execution halted
Traceback (most recent call last):
File “/home/yjk/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 234, in denoise_paired
run_commands([cmd])
File “/home/yjk/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/yjk/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/tmpui69c8hs/forward’, ‘/tmp/tmpui69c8hs/reverse’, ‘/tmp/tmpui69c8hs/output.tsv.biom’, ‘/tmp/tmpui69c8hs/track.tsv’, ‘/tmp/tmpui69c8hs/filt_f’, ‘/tmp/tmpui69c8hs/filt_r’, ‘0’, ‘0’, ‘0’, ‘0’, ‘2.0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/yjk/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/yjk/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-459>”, line 2, in denoise_paired
File “/home/yjk/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/yjk/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/yjk/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.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 1), please inspect stdout and stderr to learn more.
Thanks for any help.
