q2-ITSxpress: PermissionError: [Errno 13] Permission denied: 'classifier.qza'


(pooja) #1

Hello all,

I am trying to train the QIIME classifier as mentioned in the Q2-ITSxpress tutorial.

I am using the following command on the server:

qiime feature-classifier fit-classifier-naive-bayes \

–i-reference-reads unite.qza
–i-reference-taxonomy unite-taxonomy.qza
–o-classifier classifier.qza

And I am getting the following error:

Traceback (most recent call last):
File “/opt/qiime2-2018.8/bin/qiime”, line 11, in
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 722, in call
return self.main(*args, **kwargs)
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 697, in main
rv = self.invoke(ctx)
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/click/core.py”, line 535, in invoke
return callback(*args, **kwargs)
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/q2cli/commands.py”, line 294, in call
path = result.save(output)
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/qiime2/sdk/result.py”, line 148, in save
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/archiver.py”, line 347, in save
self.CURRENT_ARCHIVE.save(self.path, filepath)
File “/opt/qiime2-2018.8/lib/python3.5/site-packages/qiime2/core/archive/archiver.py”, line 162, in save
allowZip64=True) as zf:
File “/opt/qiime2-2018.8/lib/python3.5/zipfile.py”, line 1009, in init
self.fp = io.open(file, filemode)
PermissionError: [Errno 13] Permission denied: ‘classifier.qza’

I will be very grateful for any help regarding this.

(Colin Brislawn) #2

Good afternoon!

Thank you for posting that detailed log file. Let me see how I can help.

This is the main error:

and I think that has to do with this:

Looks like your account on the server does not have access to open up the classifier.qza file. Whoever set up Qiime on this server can give your account access to this file so that the command will run.

Alternatively, you could use this tutorial to install qiime yourself (so that you own all the files and don’t have any issues!)

Let me know if this works for you!