Dear all:
I met some problem when i running dada2-denoise-paired,my command is:
*qiime dada2 denoise-paired *
*--i-demultiplexed-seqs demux-paired-end-adaptcut.qza *
*--p-trim-left-f 0 *
*--p-trim-left-r 0 *
*--p-trunc-len-f 0 *
*--p-trunc-len-r 0 *
--o-table table.qza *
--o-representative-sequences rep-seqs.qza *
--o-denoising-stats denoising-stats.qza *
--p-n-threads 0 *
--verbose &
I set --p-trim-left-f/r as 0 because i already cut the adapter by the command below:
qiime cutadapt trim-paired*
** --i-demultiplexed-sequences demux-paired-end.qza*
** --p-front-f GTGYCAGCMGCCGCGGTAA*
** --p-front-r GGACTACNVGGGTWTCTAAT*
** --o-trimmed-sequences trimed-seqs-cut.qza
and my quality plot:
it seems the quality not bad, ao i set --p-trunc-len-f/r as 0,too.
I got error as follwing after enter my command:
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/tmpikjckh56/forward /tmp/tmpikjckh56/reverse /tmp/tmpikjckh56/output.tsv.biom /tmp/tmpikjckh56/track.tsv /tmp/tmpikjckh56/filt_f /tmp/tmpikjckh56/filt_r 0 0 0 0 2.0 2.0 2 independent consensus 1.0 1 1000000
*R version 3.5.1 (2018-07-02) *
Loading required package: Rcpp
*DADA2: 1.10.0 / Rcpp: 1.0.4.6 / RcppParallel: 5.0.0 *
1) Filtering ....................................................
2) Learning Error Rates
245289820 total bases in 1066855 reads from 14 samples will be used for learning the error rates.
Traceback (most recent call last):
- File "/home/mzl/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 264, in denoise_paired*
- run_commands([cmd])*
- File "/home/mzl/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands*
- subprocess.run(cmd, check=True)*
- File "/home/mzl/miniconda3/envs/qiime2-2020.8/lib/python3.6/subprocess.py", line 438, in run*
- output=stdout, stderr=stderr)*
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpikjckh56/forward', '/tmp/tmpikjckh56/reverse', '/tmp/tmpikjckh56/output.tsv.biom', '/tmp/tmpikjckh56/track.tsv', '/tmp/tmpikjckh56/filt_f', '/tmp/tmpikjckh56/filt_r', '0', '0', '0', '0', '2.0', '2.0', '2', 'independent', '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/mzl/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call*
- results = action(*arguments)
- File "", line 2, in denoise_paired*
- File "/home/mzl/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable*
- output_types, provenance)*
- File "/home/mzl/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor*
- output_views = self._callable(*view_args)
- File "/home/mzl/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 279, in denoise_paired*
- " and stderr to learn more." % e.returncode)*
Exception: An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.
Plugin error from dada2:
- An error was encountered while running DADA2 in R (return code -9), please inspect stdout and stderr to learn more.*
See above for debug info.