16S ASVs assignment against SILVA database

Hi QIIME2 users,

I’m been trying to classify my 16S ASVs/sub-OTUs representative sequences against the SILVA database (Silva 119 99% OTUs full-length sequences). To do so, I tried to use the following qiime2’s plugin:

qiime feature-classifier classify-sklearn --i-classifier silva-119-99-nb-classifier.qza --i-reads rep-seqs-dada2_ANT_FIELDS_PEN.qza --o-classification taxonomy-rep-seqs-dada2_ANT_FIELDS_PEN.qza

The SILVA database was downloaded from the “data resources” link available in QIIME2 website.

However, I got the following error:

Traceback (most recent call last):
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
results = action(**arguments)
File "<decorator-gen-272>", line 2, in classify_sklearn
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 225, in bound_callable
spec.view_type, recorder)
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/result.py", line 265, in _view
result = transformation(self._archiver.data_dir)
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/core/transform.py", line 70, in transformation
new_view = transformer(view)
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/site-packages/q2_feature_classifier/_taxonomic_classifier.py", line 71, in _1
tar.extractall(dirname)
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/tarfile.py", line 1998, in extractall
numeric_owner=numeric_owner)
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/tarfile.py", line 2040, in extract
numeric_owner=numeric_owner)
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/tarfile.py", line 2110, in _extract_member
self.makefile(tarinfo, targetpath)
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/tarfile.py", line 2158, in makefile
copyfileobj(source, target, tarinfo.size, ReadError)
File "/home/ciimar/miniconda3/envs/qiime2-2018.4/lib/python3.5/tarfile.py", line 244, in copyfileobj
dst.write(buf)
OSError: [Errno 28] No space left on device

I’m running this in a server, and currently this server has around 500 Gb of free storage, so it’s difficult to believe that I do not have enough storage. Unfortunately, I do not understand the source of error in order to fix it. I run the same but using the GreenGenes database (Greengenes 13_8 99% OTUs full-length sequences) and it works well.

Please, can anyone help me on this issue?

Thanks in advance!
António

Hi @antonioggsousa!

I suspect your server doesn’t have 500gb free for the /tmp/ partition which is what QIIME 2 will use by default.

Try setting this environment variable (after updating the path) before running your command and see if that helps:

export TMPDIR=/path/to/somemwhere/with/lots/of/free/disk/

Hopefully that works!

2 Likes

Thank you @ebolyen! It works perfectly!

Cheers,
António

1 Like

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