[swadmin@sirius ~/qiime2]$ echo $TMPDIR
/scratch/swadmin
The following is the logile info
[swadmin@sirius ~/qiime2]$ more /scratch/swadmin/qiime2-q2cli-err-8t9fs51h.log
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 /scratch/swadmin/tmpghjjbq5k/forward /scratch/swadmin/tmpghjjbq5k/reverse /scratch/swadmin/tmpghjjbq5k/output.tsv.biom /scratch/swadmin/tmpghjjbq5k/track.tsv /scratch/swad
min/tmpghjjbq5k/filt_f /scratch/swadmin/tmpghjjbq5k/filt_r 150 150 5 5 2.0 2 consensus 1.0 1 1000000
Traceback (most recent call last):
File “/gsfs0/public/qiime/miniconda3/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 “/gsfs0/public/qiime/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/qiime2/sdk/action.py”, line 232, in bound_callable
output_types, provenance)
File “/gsfs0/public/qiime/miniconda3/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 “/gsfs0/public/qiime/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 229, in denoise_paired
run_commands([cmd])
File “/gsfs0/public/qiime/miniconda3/envs/qiime2-2018.6/lib/python3.5/site-packages/q2_dada2/_denoise.py”, line 36, in run_commands
subprocess.run(cmd, check=True)
File “/gsfs0/public/qiime/miniconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 383, in run
with Popen(*popenargs, **kwargs) as process:
File “/gsfs0/public/qiime/miniconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 676, in init
restore_signals, start_new_session)
File “/gsfs0/public/qiime/miniconda3/envs/qiime2-2018.6/lib/python3.5/subprocess.py”, line 1289, in _execute_child
raise child_exception_type(errno_num, err_msg)
FileNotFoundError: [Errno 2] No such file or directory: ‘run_dada_paired.R’
Would you point me the path of the 'run_dada_paired.R" in qiime2 package? It seems the program can’t find it.
Thanks!
Wei