Hello Qiime2 team,
I am using qiime2-2019.10 and got the following error using qiime dada2 denoise-paired command:
*****below is complete error
Command:
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-paired-end.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 245 --p-trunc-len-r 245 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 0 --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/tmpcqewjq9m/forward /tmp/tmpcqewjq9m/reverse /tmp/tmpcqewjq9m/output.tsv.biom /tmp/tmpcqewjq9m/track.tsv /tmp/tmpcqewjq9m/filt_f /tmp/tmpcqewjq9m/filt_r 248 248 0 0 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 sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE)) :
write error, closing pipe to the master
Error in names(answer) <- names1 :
'names' attribute [104] must be the same length as the vector [102]
Execution halted
Traceback (most recent call last):
File "/home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 257, in denoise_paired
run_commands([cmd])
File "/home/scebmeta/bin/miniconda3/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/scebmeta/bin/miniconda3/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/tmpcqewjq9m/forward', '/tmp/tmpcqewjq9m/reverse', '/tmp/tmpcqewjq9m/output.tsv.biom', '/tmp/tmpcqewjq9m/track.tsv', '/tmp/tmpcqewjq9m/filt_f', '/tmp/tmpcqewjq9m/filt_r', '248', '248', '0', '0', '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/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/q2cli/commands.py", line 328, in call
results = action(**arguments)
File "</home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/decorator.py:decorator-gen-463>", line 2, in denoise_paired
File "/home/scebmeta/bin/miniconda3/envs/qiime2-2019.10/lib/python3.6/site-packages/qiime2/sdk/action.py", line 240, in bound_callable
output_types, provenance)
File "/home/scebmeta/bin/miniconda3/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/scebmeta/bin/miniconda3/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.
Please help me to solve this issue,
Thanks in advance,
Khemlal
