Hello! When I used "qiime dada2 denoise-paired", it gives an error:
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/tmplvmoaop5/forward /tmp/tmplvmoaop5/reverse /tmp/tmplvmoaop5/output.tsv.biom /tmp/tmplvmoaop5/track.tsv /tmp/tmplvmoaop5/filt_f /tmp/tmplvmoaop5/filt_r 284 279 0 0 2.0 2.0 2 consensus 1.0 36 1000000
R version 3.5.1 (2018-07-02)
Loading required package: Rcpp
DADA2: 1.10.0 / Rcpp: 1.0.3 / RcppParallel: 4.4.4
- Filtering Error in sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) :
write error, closing pipe to the master
Error in names(answer) <- names1 :
'names' attribute [71] must be the same length as the vector [47]
Execution halted
Traceback (most recent call last):
File "/home/ccllab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/home/ccllab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/home/ccllab/miniconda3/envs/qiime2-2020.2/lib/python3.6/subprocess.py", line 418, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmplvmoaop5/forward', '/tmp/tmplvmoaop5/reverse', '/tmp/tmplvmoaop5/output.tsv.biom', '/tmp/tmplvmoaop5/track.tsv', '/tmp/tmplvmoaop5/filt_f', '/tmp/tmplvmoaop5/filt_r', '284', '279', '0', '0', '2.0', '2.0', '2', 'consensus', '1.0', '36', '1000000']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/ccllab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</home/ccllab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/decorator.py:decorator-gen-455>", line 2, in denoise_paired
File "/home/ccllab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/home/ccllab/miniconda3/envs/qiime2-2020.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/home/ccllab/miniconda3/envs/qiime2-2020.2/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.
I encountered this problem for the first time,and I don't know how to solve this problem,does anyone know? I would appreciate!
And here is command:
qiime dada2 denoise-paired \
--i-demultiplexed-seqs primer-trimmed-demux_16S_PE.qza \
--p-trim-left-f 0 \
--p-trim-left-r 0 \
--p-trunc-len-f 284 \
--p-trunc-len-r 279 \
--p-n-threads 36 \
--o-representative-sequences dada2_denoising//rep-seqs-dada2.qza \
--o-table dada2_denoising//table-dada2.qza \
--o-denoising-stats dada2_denoising/stats-dada2.qza