Thank you very much! I have carefully examined the forward and reverse sequence files, which is exactly what you said. Thank you for your guidance! After I corrected and rerun, I encountered the following problems:
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/tmpleij8bax/forward /tmp/tmpleij8bax/reverse /tmp/tmpleij8bax/output.tsv.biom /tmp/tmpleij8bax/track.tsv /tmp/tmpleij8bax/filt_f /tmp/tmpleij8bax/filt_r 0 0 23 26 2.0 2.0 2 consensus 1.0 8 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
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Filtering …
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Learning Error Rates
256591361 total bases in 1043204 reads from 16 samples will be used for learning the error rates.
253821236 total bases in 1043204 reads from 16 samples will be used for learning the error rates.
- Denoise remaining samples …Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
.Duplicate sequences in merged output.
.Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
…Duplicate sequences in merged output.
.Duplicate sequences in merged output.
…Traceback (most recent call last):
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2_dada2/_denoise.py”, line 234, in denoise_paired
run_commands([cmd])
File “/home/hef/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/hef/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/tmpleij8bax/forward’, ‘/tmp/tmpleij8bax/reverse’, ‘/tmp/tmpleij8bax/output.tsv.biom’, ‘/tmp/tmpleij8bax/track.tsv’, ‘/tmp/tmpleij8bax/filt_f’, ‘/tmp/tmpleij8bax/filt_r’, ‘0’, ‘0’, ‘23’, ‘26’, ‘2.0’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘8’, ‘1000000’]’ died with <Signals.SIGKILL: 9> .
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/q2cli/commands.py”, line 327, in call
results = action(**arguments)
File “</home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/decorator.py:decorator-gen-459>”, line 2, in denoise_paired
File “/home/hef/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 240, in bound_callable
output_types, provenance)
File “/home/hef/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/hef/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 -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.
Is this because of insufficient memory? I hope to get your guidance again. Thank you!