PermissionError: [Errno 13]

Hi everyone! I’m starting to use qiime2, and I have an issue when trying to visualize imported data with manifest:

qiime demux summarize --i-data /demux-paired-summary.qza --o-visualization /demux-paired-summary.qzv

That are the command lines qiime2 sent back to me:

File “/home/qiime2/miniconda/envs/qiime2-2018.2/bin/qiime”, line 11, in
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/click/”, line 722, in call
return self.main(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/click/”, line 697, in main
rv = self.invoke(ctx)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/click/”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/click/”, line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/click/”, line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/click/”, line 535, in invoke
return callback(*args, **kwargs)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/q2cli/”, line 263, in call
path =
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/sdk/”, line 143, in save
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/core/archive/”, line 341, in save, filepath)
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/site-packages/qiime2/core/archive/”, line 161, in save
allowZip64=True) as zf:
File “/home/qiime2/miniconda/envs/qiime2-2018.2/lib/python3.5/”, line 1009, in init
self.fp =, filemode)
PermissionError: [Errno 13] Permission denied: ‘/demux-paired-summary.qzv’

Thanks in advance!

Hi @Manuss_Ponce!

You are telling QIIME 2 to save the output to the path / with the filename demux-paired-summary.qzv (that is this part of your command --o-visualization /demux-paired-summary.qzv). The path / is the root of your filesystem, and on virtually all machines is protected such that only administrative users can write to that location. Drop the / from your command it it will then save the file demux-paired-summary.qzv to whatever your current working directory is:

qiime demux summarize --i-data /demux-paired-summary.qza --o-visualization demux-paired-summary.qzv

Hope that helps! :t_rex: :qiime2:

You’re right!! Now it works. Thanks a lot :wink:

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