Thanks
I think I have installed this successfully. ( I remember I have gone through this first time as well)
Verifying transaction: done
Executing transaction: - Enabling notebook extension jupyter-js-widgets/extension...
- Validating: OK
done
To activate this environment, use:
> source activate qiime2-2019.1
To deactivate an active environment, use:
> source deactivate
I qsub a pbs file. I have the same error
[qiuwa@sirius qiime2]$ more /scratch/qiuwa/qiime2-q2cli-err-0kdnj7tn.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/qiuwa/tmpcjsadpp8/forward /scratch/qiuwa/tmpcjsadpp8/reverse /scratch/qiuwa/tmpcjsadpp8/output.tsv.biom /scratch/qiuwa/tmpcjsadpp8/track.tsv /scratch/qiuwa/tmpcjs
adpp8/filt_f /scratch/qiuwa/tmpcjsadpp8/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)
PermissionError: [Errno 13] Permission denied
somehow I had error for running:
[swadmin@sirius qiime] source activate qiime2-2019.1
activate: No such file or directory.
[swadmin@sirius qiime] which activate
/usr/public/qiime/miniconda3//bin/activate
Should I put "source activate qiime2-2019.1" inside pbs file?
I run the following on the terminal. I had the same error.
[qiuwa@sirius qiime2]$ qiime dada2 denoise-paired
? --i-demultiplexed-seqs demux.qza
? --p-trim-left-f 5
? --p-trim-left-r 5
? --p-trunc-len-f 150
? --p-trunc-len-r 150
? --o-table table.qza
? --o-representative-sequences rep-seqs.qza
? --o-denoising-stats denoising-stats.qza
Plugin error from dada2:
[Errno 13] Permission denied
Debug info has been saved to /scratch/qiuwa/qiime2-q2cli-err-a7mwxm5i.log
Thanks
Wei