I am currently working with qiime2 version 2023.7 on ubuntu. It has always worked well and never given me any problems until this week. Today I tried to use it for doing a feature table summarize (code: qiime feature-table summarize --i-table table.qza --o-visualization table_p.qzv --m-sample-metadata-file metadata_new.txt) and it gave me this strange error:
There was a problem loading 'table.qza' as an artifact:
It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'FeatureTable[Frequency]' and format 'BIOMV210DirFmt'
See above for debug info.
I can't understand what this is because I always used this kind of codes and never gave me any problem, even when weeks ago I did almost the same thing using another metadata and the exact same table.qza.
Hi @Federico_Rossignoli,
I am sorry to hear that you are running into errors! We will definitely get to the bottom of it!
This typically happens when something goes wrong with the qiime2 installation. Lets check a couple things!
First, Can you run qiime tools validate on your table.qza and report the result?
Second, Did you mac sure that you installed the linux version of this most recent qiime2 release?
Third, Is this a fresh install of the new release or have you installed community plugins in to the env as well?
I ran the code it asked for and it gave me this error.
qiime tools validate table.qza
Traceback (most recent call last):
File "/home/loris-ws/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/builtin/tools.py", line 664, in validate
result = qiime2.sdk.Result.load(path)
File "/home/loris-ws/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/result.py", line 74, in load
cache = get_cache()
File "/home/loris-ws/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/cache.py", line 113, in get_cache
_CACHE.temp_cache = Cache()
File "/home/loris-ws/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/cache.py", line 379, in new
path = _get_temp_path()
File "/home/loris-ws/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/cache.py", line 158, in _get_temp_path
raise ValueError(f"Directory '{cache_dir}' already exists without "
ValueError: Directory '/tmp/qiime2' already exists without proper permissions '0o41777' set. Current permissions are '0o40777.' This most likely means something other than QIIME 2 created the directory '/tmp/qiime2' or QIIME 2 failed between creating '/tmp/qiime2' and setting permissions on it.
There was a problem loading table_14_age.qza as a QIIME 2 Result:
Directory '/tmp/qiime2' already exists without proper permissions '0o41777' set. Current permissions are '0o40777.' This most likely means something other than QIIME 2 created the directory '/tmp/qiime2' or QIIME 2 failed between creating '/tmp/qiime2' and setting permissions on it.
See above for debug info.
Very strange, it seems like a permissions problem but up until now it had always worked well. I actually worked on it until last week with no problems
2) The version I have been working with in recent months, and with which I would like to continue working at least until the end of the current project, is the qiime-2023.7 version. I also tried reinstalling it with another name but it doesn't install successfully.
3) I installed it a few months ago, I don't think there are any plugins installed, perhaps only the picrust2 one.
The /tmp/qiime2 directory is the location of the cache QIIME 2 uses to track intermediate results it creates. Yours somehow has the incorrect permissions set on it. I'm not sure how or why that happened, but it is at least responsible for the:
Directory '/tmp/qiime2' already exists without proper permissions
portion of what you're seeing.
Can you run ls -al /tmp/qiime2/loris-ws? Additionally, do you know if anyone else using the workstation you're on uses QIIME 2, and does anyone else use the account with the username loris-ws? The easiest way to resolve this issue would be to delete the /tmp/qiime2 directory and let QIIME 2 remake it, but I'm trying to make sure we won't be deleting anyone's work if we do that. Given that this directory is under tmp though, you are probably safe to remove it.
total 28
drwxrwxrwx 6 loris-ws loris-ws 4096 feb 19 15:32 .
drwxrwxrwx 3 loris-ws loris-ws 4096 feb 19 15:28 ..
drwxrwxrwx 2 loris-ws loris-ws 4096 feb 19 15:32 data
drwxrwxrwx 2 loris-ws loris-ws 4096 feb 19 15:32 keys
drwxrwxrwx 2 loris-ws loris-ws 4096 feb 19 15:32 pools
drwxrwxrwx 2 loris-ws loris-ws 4096 feb 19 15:32 processes
-rwxrwxrwx 1 loris-ws loris-ws 37 feb 19 15:32 VERSION
I haven't deleted the /tmp/qiime2 directory yet because I wanted to send you this before, please tell me if everything's fine so I will proceed. Yes there is someone else that works with same account on the ws but not on qiime2 at the moment (Just on R, can this have caused the problem somehow..?).
Thank you so much for the help you are giving me,
Federico
As far as I am aware no, that should not have caused the problem. If you have established that no one else has been using QIIME 2 on that machine lately, then you should be safe to remove that /tmp/qiime2 directory.
I can't really figure out what happened but now that I removed that directory it seems to work. Thanks so much. I will confirm that everything works next week when I run all the steps again. In any case, thanks again so much for the support. It was really very useful.