Hello everybody,
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
provenance.add_input(name, artifact)
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
shutil.copytree(
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 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.
Hello Collin,
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.
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
I´ll try next week.