No Space Left on Device for qiime feature-classifier

[mwang87 (Mingxun Wang)]

I am running qiime feature-classifier on a computer with plenty of hard disk space however I get this error:

Traceback (most recent call last):
File “/local_tools/conda/miniconda3/envs/qiime2-2017.11/lib/python3.5/tarfile.py”, line 2158, in makefile
copyfileobj(source, target, tarinfo.size, ReadError)
File “/local_tools/conda/miniconda3/envs/qiime2-2017.11/lib/python3.5/tarfile.py”, line 244, in copyfileobj
dst.write(buf)
OSError: [Errno 28] No space left on device

This desktop is a 32 core 256GB machine with 1TB free of hard disk space.

I am using this command:

source /local_tools/conda/miniconda3/bin/activate qiime2-2017.11
qiime feature-classifier classify-sklearn --i-classifier silva-119-99-nb-classifier.qza --i-reads --o-classification --p-n-jobs 1

This classifier is from qiime2 website.

I suspect from the command line that qiime2 is attempting to put a temporary file somewhere that I do not control and that space has no space.

Any help would be appreciated.

–Ming

[thermokarst]

Hi @mwang87!

@mwang87

I suspect from the command line that qiime2 is attempting to put a temporary file somewhere that I do not control and that space has no space.

I think you're right! QIIME 2 will use the temp dir wherever python tell it to go, that is in the TMPDIR environment variable, usually.

What does it say when you run:

$ echo $TMPDIR

?

If you have a better location, you can override it by setting that environment variable yourself before running QIIME 2 commands. Keep me posted!

[mwang87 (Mingxun Wang)]

Thanks! That worked!