Hi
Sorry for only getting back to you now, couldnt locate the err file, this is the error I got
Traceback (most recent call last):
File “/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 229, in denoise_paired
run_commands([cmd])
File “/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 398, in run
output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command ‘[‘run_dada_paired.R’, ‘/var/tmp/pbs.1484090.sched01/tmpzb83710l/forward’, ‘/var/tmp/pbs.1484090.sched01/tmpzb83710l/reverse’, ‘/var/tmp/pbs.1484090.sched01/tmpzb83710l/output.tsv.biom’, ‘/var/tmp/pbs.1484090.sched01/tmpzb83710l/track.tsv’, ‘/var/tmp/pbs.1484090.sched01/tmpzb83710l/filt_f’, ‘/var/tmp/pbs.1484090.sched01/tmpzb83710l/filt_r’, ‘300’, ‘280’, ‘19’, ‘20’, ‘2.0’, ‘2’, ‘consensus’, ‘1.0’, ‘1’, ‘1000000’]’ returned non-zero exit status 1
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2cli/commands.py”, line 274, in call
results = action(**arguments)
File “”, line 2, in denoise_paired
File “/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 232, in bound_callable
output_types, provenance)
File “/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 367, in callable_executor
output_views = self._callable(**view_args)
File “/apps/chpc/bio/anaconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 244, 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.
Thanks for your assistance