OSEError : (Errno 122) Disk Quota Exceeded

[krupathakkar]

Hi All,

I have been trying to download QIIME2 2021.8 or 4 so that I can use the SILVA138 classifier on the updated sklearn. I am using a remote cluster and have been doing the native download. One of the issues I am getting is below when I try to activate my environment.

OSError: [Errno 122] Disk quota exceeded

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/software/anaconda3/envs/qiime2-2021.4/bin/qiime", line 11, in
sys.exit(qiime())
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 829, in call
return self.main(*args, **kwargs)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 781, in main
with self.make_context(prog_name, args, **extra) as ctx:
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 700, in make_context
self.parse_args(ctx, args)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
return super().parse_args(ctx, args)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1209, in parse_args
echo(ctx.get_help(), color=ctx.color)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 570, in get_help
return self.command.get_help(self)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 975, in get_help
self.format_help(ctx, formatter)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/click/core.py", line 1003, in format_help
self.format_options(ctx, formatter)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/click/command.py", line 157, in format_options
for subcommand in self.list_commands(ctx):
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 92, in list_commands
plugins = sorted(self._plugin_lookup)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
import q2cli.core.cache
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/core/cache.py", line 406, in
CACHE = DeploymentCache()
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in init
self._state = self._get_cached_state(refresh=refresh)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
self._cache_current_state(current_requirements)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/core/cache.py", line 200, in _cache_current_state
state = self._get_current_state()
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2cli/core/cache.py", line 238, in _get_current_state
plugin_manager = qiime2.sdk.PluginManager()
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 54, in new
self._init(add_plugins=add_plugins)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 81, in _init
plugin = entry_point.load()
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pkg_resources/init.py", line 2472, in load
return self.resolve()
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/pkg_resources/init.py", line 2478, in resolve
module = import(self.module_name, fromlist=['name'], level=0)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_sample_classifier/plugin_setup.py", line 20, in
from q2_feature_table import heatmap_choices
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_feature_table/init.py", line 12, in
from ._summarize import (summarize, tabulate_seqs)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_feature_table/_summarize/init.py", line 9, in
from ._visualizer import (summarize, tabulate_seqs)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/q2_feature_table/_summarize/_visualizer.py", line 16, in
import seaborn as sns
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/seaborn/init.py", line 2, in
from .rcmod import * # noqa: F401,F403
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/seaborn/rcmod.py", line 7, in
from . import palettes
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/seaborn/palettes.py", line 9, in
from .utils import desaturate, get_color_cycle
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/seaborn/utils.py", line 14, in
import matplotlib.pyplot as plt
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/matplotlib/pyplot.py", line 36, in
import matplotlib.colorbar
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/matplotlib/colorbar.py", line 38, in
from matplotlib import _api, collections, cm, colors, contour, ticker
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/matplotlib/contour.py", line 17, in
import matplotlib.font_manager as font_manager
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/matplotlib/font_manager.py", line 1443, in
fontManager = _load_fontmanager()
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/matplotlib/font_manager.py", line 1438, in _load_fontmanager
json_dump(fm, fm_path)
File "/software/anaconda3/envs/qiime2-2021.4/lib/python3.8/site-packages/matplotlib/font_manager.py", line 990, in json_dump
_log.warning('Could not save font_manager cache {}'.format(e))
OSError: [Errno 122] Disk quota exceeded

I have cleared out the tmp directory, there is space in my home directory as well and the working directory. I have also tried using previous versions such as 2020.2 and that works fine

Not too sure what to do next

[timanix (Timur Yergaliyev)]

Hello and welcome to the forum!
According to this reply, you may run out of the space in your home directory or temp directory.

@krupathakkar

I have cleared out the tmp directory,

If it did not work for you, could you try to clean your conda?

conda clean --all

This will remove all unused packages and caches and free some space. If your home directory is close to the limit deleting unused environments and installed tools could also be helpful. Or contact cluster admins if they can increase your quota.

[krupathakkar]

Hello and thank you for your quick reply!

I actually just tried that and the same error came back again when I tried to conda activate. Would it be worth removing the environment and redownloading it? I have tried i

Also is QIIME2 2021.4 much larger than QIIME2 2020?

[timanix (Timur Yergaliyev)]

@krupathakkar

Would it be worth removing the environment and redownloading it?

It would be a good idea to try to delete all failed environments and unnecessary or outdated tools/files and then to clean conda to delete all unused packages. Also, check your home directory on the presence of large core.* files, which are produced on the server when some jobs are crashed in the past. If the error still persist, probably you should contact clusters admins. In my case my quota was increased by the admins when I run out of space, though It wasn't due to Qiime2 installation.

[krupathakkar]

Hello!

I did try that again and cleared out some space actually though the same error message appeared unfortunately.

As a potential back up - I could try and use Docker for my installation though my cluster for security only allows Singularity (there is no updated singularity script for the most recent version of QIIME2), would this disk space also be an issue then?

[timanix (Timur Yergaliyev)]

That's seems to be a little bit strange to me. Of course you can try with Docker and if it is works, then the problem not in space, but some kind of misterious compatibility issues.
Beside installing Docker, other options are:

1. Use older version of Qiime2 (with older sklearn classifier)
2. Try to install conda and Qiime2 into your working space instead of home directory.
3. Add some Gb to your home quota.

If other mods have better ideas please add your suggestions

[krupathakkar]

Hi!

So asking for extra space in my home worked! Eventhough I had space already, I think I needed more for the initial caching stage. Thank you very much!