Hello, I am using 2019.4 version of Qiime2 in virtualbox. Couldn’t find in the forum.
Any command I try to run shows me error:
OSError: [Errno 30] Read-only file system
and after rebooting a windows pop up:
An error has occurred during virtual machine execution! The error details are shown below. You may try to correct the error and resume the virtual machine execution.
Unable to allocate and lock memory. The virtual machine will be paused. Please close applications to free up memory or close the VM.
Welcome to the forum! Unfortunately I don’t know for sure what is going on. One option is your virtual machine is still stuck with the default amount of memory (or perhaps less if the platform is that unstable).
Does this error occur on a fresh boot from the host machine? What operating system is your host machine?
OS is windows 7.
I reassigned a greater memory in the configuration of the virtual image.
And yes, I tried rebooting both the host machine and virtual box.
Traceback (most recent call last):
File “/home/qiime2/miniconda/envs/qiime2-2019.4/bin/qiime”, line 11, in
sys.exit(qiime())
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 1132, in invoke
cmd_name, cmd, args = self.resolve_command(ctx, args)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/click/core.py”, line 1171, in resolve_command
cmd = self.get_command(ctx, cmd_name)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 99, in get_command
plugin = self._plugin_lookup[name]
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/commands.py”, line 75, in _plugin_lookup
import q2cli.core.cache
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 400, in
CACHE = DeploymentCache()
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 58, in init
self._cache_dir = self._get_cache_dir()
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/site-packages/q2cli/core/cache.py”, line 85, in _get_cache_dir
os.makedirs(cache_dir, exist_ok=True)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/os.py”, line 210, in makedirs
makedirs(head, mode, exist_ok)
File “/home/qiime2/miniconda/envs/qiime2-2019.4/lib/python3.6/os.py”, line 220, in makedirs
mkdir(name, mode)
OSError: [Errno 30] Read-only file system: ‘/home/qiime2/.config/q2cli’
This is the full error message that I get over and over again
Thanks for your help
I’m very sorry I lost track of this. Based on the error it seems like root took over the ~/.config/q2cli directory. I suspect sudo may be to blame, but it’s hard to say. If you run this what does it say:
ls -al ~/.config/q2cli
Also, it is worth noting that this path seems like it predates a change in where we store the config now. You may consider just updating to the latest virtualbox image which will have QIIME 2 2019.7 installed, as it looks like something may be acting really strangely.