Hi,
I am analyzing my 16s data and encounter a problem at the denoise step. I am using qiime2/2021.2 version. I did cutadapt to remove primer. The code was working perfectly for me 2 years ago, not sure why it doesnt work this time. I did all the coding on an interactive mode.
The following is my code and error message.
jiang329@acl08 [~/Jan_steffan/Gallaher_Project_012/primer_removed/merged] % qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux.qza
--p-trunc-len-f 200
--p-trunc-len-r 100
--p-max-ee-f 3
--p-max-ee-r 3
--o-representative-sequences rep-seqs.qza
--o-table table.qza
--o-denoising-stats stats.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/tmpkhfvhror/forward /tmp/tmpkhfvhror/reverse /tmp/tmpkhfvhror/output.tsv.biom /tmp/tmpkhfvhror/track.tsv /tmp/tmpkhfvhror/filt_f /tmp/tmpkhfvhror/filt_r 200 100 0 0 3.0 3.0 2 independent consensus 1.0 1 1000000
Rscript execution error: No such file or directory
Traceback (most recent call last):
File "/common/software/install/migrated/qiime2/2021.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 264, in denoise_paired
run_commands([cmd])
File "/common/software/install/migrated/qiime2/2021.2/lib/python3.6/site-packages/q2_dada2/_denoise.py", line 36, in run_commands
subprocess.run(cmd, check=True)
File "/common/software/install/migrated/qiime2/2021.2/lib/python3.6/subprocess.py", line 438, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command '['run_dada_paired.R', '/tmp/tmpkhfvhror/forward', '/tmp/tmpkhfvhror/reverse', '/tmp/tmpkhfvhror/output.tsv.biom', '/tmp/tmpkhfvhror/track.tsv', '/tmp/tmpkhfvhror/filt_f', '/tmp/tmpkhfvhror/filt_r', '200', '100', '0', '0', '3.0', '3.0', '2', 'independent', 'consensus', '1.0', '1', '1000000']' returned non-zero exit status 255.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/common/software/install/migrated/qiime2/2021.2/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call
results = action(**arguments)
File "", line 2, in denoise_paired
File "/common/software/install/migrated/qiime2/2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
output_types, provenance)
File "/common/software/install/migrated/qiime2/2021.2/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in callable_executor
output_views = self._callable(**view_args)
File "/common/software/install/migrated/qiime2/2021.2/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 255), please inspect stdout and stderr to learn more.
Plugin error from dada2:
An error was encountered while running DADA2 in R (return code 255), please inspect stdout and stderr to learn more.
See above for debug info.