I´m a new qiime2 user and low-experienced bioinformatician so (I hope) this question may be easy to solve. When I run ' qiime feature-classifier classify-sklearn ' command, it doesn´t work. This is the exact message:
Plugin error from feature-classifier:
[Errno 2] No such file or directory: '/tmp/qiime2/vmunoz/data/2bbe61fa-7f78-4913-a6a7-b42e6fff2279/provenance'
Debug info has been saved to /tmp/qiime2-q2cli-err-8_beyezv.log
When i open this log file, it content is:
Traceback (most recent call last):
File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/q2cli/commands.py", line 339, in call
results = action(**arguments)
File "", line 2, in classify_sklearn
File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/sdk/action.py", line 210, in bound_callable
File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/provenance.py", line 425, in add_input
self.inputs[name] = self.add_ancestor(input)
File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/site-packages/qiime2/core/archive/provenance.py", line 167, in add_ancestor
File "/opt/anaconda3/envs/qiime2-2022.8/lib/python3.8/shutil.py", line 555, in copytree
with os.scandir(src) as itr:
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/qiime2/vmunoz/data/2bbe61fa-7f78-4913-a6a7-b42e6fff2279/provenance'
I have seen some simmilar problems in the forum but none of them are reported for my qiime2 version (2022.8 installed from conda in my organization´s minicluster). In this thread I read obout the possibility of a agressive /tmp cleaning by my computer admin, but I dont really know if this is the real problem.
Thank you for your time,
Welcome to the forums!
Thank you for posting your full error. The missing path is an important clue:
If an input file was missing, it would look like this
No such file or directory: '/home/vmunoz/your-input-file.qza'
The fact that the missing file is in
/tmp leads to this conclusion:
You can set /tmp to a different location, or reach out to your cluster admins about their /tmp settings. They should be able to tell you how they have set up /tmp to work, and if this could be causing the problem we suspect.
Keep us posted!
Thank you very much for your speed in answering my question. I will ask my computer admin for help and if it get solved, I´ll let you know. Until then, I´ll try to do the analysis in a local computer.
I have just noticed that the folder "2bb61fa-7f78-4913-a6a7-b42e6fff2279" came from the Silva 138 99% OTUs full-length sequences pre-trained classifier. I tried to unzip the classifier in order to see what are in, and one of the resulting directories is 2bb6qfa..... Do you find it relevant? If this classifier were "broken", i suppose many people would have reported it.
Thank you again,
If this classifier were "broken", i suppose many people would have reported it.
Yes, I would suspect that as well. But you never know!
The temp air still makes me think it's related to your HPC setup. While I was away, did you hear back from your HPC team about how they set up /tmp on their cluster?
Unfortunately no, they are so busy I´ll try next week.
Just for trying, I run the command using the classifier trained with 515F/806R sequences and it worked perfectly. Since I have 18S sequences too, I took the "challenge" of training my own classifiers and they are also working well. I don´t know if it is a clue, but the only classifier that gives me the error message is Silva 138 99% OTUs full-length sequences
Thanks for your help!
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