I have setup a linux machine with Qiime2-2020.8 via miniconda environment as @thermokarst recommended last year. (accessible installation on /opt/miniconda/…). It worked just fine during the bioinformatics course last year (with a 2019 edition of qiime and a silva-132 classifiers). This year I have roughly the same number of students in my course (10) but I a using the silva-138-99-nb-classifiers from your website with q2-2020.8 on the same linux machine (CentOS7). But now we ran into /tmp issues telling me that there is to less space avaialble for the users. The problematic step si: qiime feature-classifier classify-sklearn; each student used only one thread since I was aware that the new classifier requiresmore disk space.
I have checked it with coulleagues in out IT department, but they tell me that there is enough free disk space available.
Is there any setting in q2 that I should consider to change in order to get it running?
The number of reads is not too high, ca. 16,500 freatures (ASVs from dada2) with ca. 4 Mio reads in 20 samples. My system has 12 cores and 128 GB RAM.
Do you have any suggestion how to improve performance of the analysis?
Traceback (most recent call last):
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2cli/commands.py”, line 329, in call
results = action(**arguments)
File “”, line 2, in classify_sklearn
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/action.py”, line 234, in bound_callable
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/sdk/result.py”, line 289, in _view
result = transformation(self._archiver.data_dir)
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/qiime2/core/transform.py”, line 70, in transformation
new_view = transformer(view)
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/site-packages/q2_feature_classifier/_taxonomic_classifier.py”, line 71, in _1
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/tarfile.py”, line 2010, in extractall
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/tarfile.py”, line 2052, in extract
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/tarfile.py”, line 2122, in _extract_member
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/tarfile.py”, line 2171, in makefile
copyfileobj(source, target, tarinfo.size, ReadError, bufsize)
File “/opt/miniconda3/envs/qiime2-2020.8/lib/python3.6/tarfile.py”, line 252, in copyfileobj
OSError: [Errno 28] No space left on device