Missing plugin(s) necessary to load Artifact error

Technical Support
1

I am receiving the error message:

"It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'FeatureData[Sequence]' and format 'DNASequencesDirectoryFormat'".

When I enter this command:

$ qiime feature-table summarize --i-table RP4_representative-sequences.qza --o-visualization RP4_test-vis.qza

This Artifact type and format are what is expected for the feature-table summarize command though. I get essentially the same error with any other command I try though. I have been able to run these commands successfully on the same files on another computer but recently switched to a virtual machine so I expect it has something to do with that... I am running Qiime 2 version 2024.2.0 through conda.

Here is the full text I receive after entering the command:

Traceback (most recent call last):

File "/home/zwl1/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/util.py", line 492, in _load_input_file
artifact = qiime2.sdk.Result.load(fp)
File "/home/zwl1/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/sdk/result.py", line 74, in load
cache = get_cache()
File "/home/zwl1/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/cache.py", line 113, in get_cache
_CACHE.temp_cache = Cache()
File "/home/zwl1/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/qiime2/core/cache.py", line 379, in new
path = _get_temp_path()
File "/home/zwl1/miniconda3/envs/qiime2-amplicon-2024.2/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 '/home/zwl1/mymount/ls58/Zach/data/qiime2' already exists without proper permissions '0o41777' set. Current permissions are '0o40755.' This most likely means something other than QIIME 2 created the directory '/home/zwl1/mymount/ls58/Zach/data/qiime2' or QIIME 2 failed between creating '/home/zwl1/mymount/ls58/Zach/data/qiime2' and setting permissions on it.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/home/zwl1/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/click/type.py", line 116, in _convert_input
result, error = q2cli.util._load_input(value)
File "/home/zwl1/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/util.py", line 397, in _load_input
artifact, error = _load_input_file(fp)
File "/home/zwl1/miniconda3/envs/qiime2-amplicon-2024.2/lib/python3.8/site-packages/q2cli/util.py", line 498, in _load_input_file
raise ValueError(
ValueError: It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'FeatureData[Sequence]' and format 'DNASequencesDirectoryFormat'

There was a problem loading 'RP4_representative-sequences.qza' as an artifact:

It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'FeatureData[Sequence]' and format 'DNASequencesDirectoryFormat'

See above for debug info.

Thanks,
Zach

2

Hello @Zach_LaTurner, do you share this computer with other people? If so, can you run ls -al /home/zwl1/mymount/ls58/Zach/data/qiime2 and post the contents here? If not, can you please remove the /home/zwl1/mymount/ls58/Zach/data/qiime2 directory and try to rerun the command? Thank you.

4

I do not share it with other people. But there are two ways that I can access the virtual machine, one is through a GUI and another way is by logging in via command line.

If I remove that directory I still get the same error. Possibly related, I was having memory issues on the virtual machine when I was running the feature-classifier command. The solution I found online was to redirect the temporary files to a mounted server. The errors I am talking about now started directly after that, but I stopped having memory issues when I made that change. Sorry if terminology doesn't make sense, not a programmer by training.

1 Like
5

Yes that probably has something to do with it. Can you try running chmod 1777 /home/zwl1/mymount/ls58/Zach/data/qiime2 then stat /home/zwl1/mymount/ls58/Zach/data/qiime2 and posting the results here?

I suspect there is something to do with the way temp is mounted that is preventing us from setting the permissions we want.

6

Ok here are the results:

File: /home/zwl1/mymount/ls58/Zach/data/qiime2
Size: 0 Blocks: 0 IO Block: 1048576 directory
Device: 2fh/47d Inode: 13200470720 Links: 2
Access: (0755/drwxr-xr-x) Uid: ( 1000/ zwl1) Gid: ( 1000/ zwl1)
Context: system_u:object_r:cifs_t:s0
Access: 2024-04-01 14:38:51.272362000 -0500
Modify: 2024-04-01 14:38:51.272362000 -0500
Change: 2024-04-01 14:38:51.272362000 -0500
Birth: 2024-04-01 14:38:51.272362000 -0500

7

That should have set the permissions on the directory to 1777, but you can see under "Access" they're still 0755. I suspect there's some kind of mask or something on the mount that's preventing the permissions from being set. I don't have much experience with this, but can you look back at how you created that mount and see if there is a way to play with the permissions?

8

Its not clear to me how to change permissions, I think I do specify read and write capabilities when I set up the mount. I will contact our IT department to see what they say.

1 Like
9

Would you happen to know how much temporary storage space the feature-classifier classify-sklearn might need? IT is going to increase my storage space to try to accomdate that so I don't have to reroute the temporary storage.

10

Unfortunately I do not have a good estimate of that. It's going to depend on how large your data is, but I couldn't tell you exactly how your input size is going to map to temp storage used.