Operation not permitted while exporting

Hi All,
Thanks for this detailed info. Unfortunately it dosen't work for me. The qza artifact looks good, but the export produces a corrupted tsv file. Thank you for your help!

(qiime2-2019.4) [email protected]:~/Desktop/shared/Single_end_QIIME2$ qiime tools export --input-path new.filtered.table.qza --output-path ./

Traceback (most recent call last):
File "/home/qiime2/miniconda/envs/qiime2-2019.4/bin/qiime", line 11, in
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/builtin/tools.py", line 55, in export_data
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/qiime2/sdk/result.py", line 137, in export_data
str(self._archiver.data_dir), str(output_dir))
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/distutils/dir_util.py", line 163, in copy_tree
File "/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/distutils/file_util.py", line 158, in copy_file
os.utime(dst, (st[ST_ATIME], st[ST_MTIME]))
PermissionError: [Errno 1] Operation not permitted

You could try giving a different output directory like “exported” instead of “./”. Or since this is a permission error you can try throwing a “sudo” in the command.

If these doesn’t work, you can extract the biom file from .qza just as it is a compressed file like a .zip file. If this method also does not work, I believe there is a problem with the .qza file.

P.S. I’m not an expert, I’m just throwing what comes to my mind here :slight_smile:

1 Like

Hi @ptpell! As @the_dummy said, it looks like this is a file permission error - you don’t appear to have permission to write to the path ~/Desktop/shared/Single_end_QIIME2. Please run the following and return the results here:

ls -lah ~/Desktop/shared/Single_end_QIIME2


An off-topic reply has been split into a new topic: exporting data: Operation not permitted

Please keep replies on-topic in the future.