Hello! I'm trying to classify some sequences of fungal ITS2, following this tutorial: Fungal ITS analysis tutorial. I'm running Qiime2-2023.7 on a server through my university. I'm very new to using servers so I'll try to answer questions about it as best as I can.
And using the UNITE database, specifically the Qiime compatible files from 7-25-2023. https://unite.ut.ee/repository.php
I downloaded the classifier that @colinbrislawn was generous enough to make and it matches the version of the UNITE files I already have: Release UNITE v9.0 v25.07.2023 for qiime2-2023.7 · colinbrislawn/unite-train · GitHub
However when I run my code
qiime feature-classifier classify-sklearn
--i-classifier unite_ver9_dynamic_25.07.2023-Q2-2023.7.qza
--i-reads Fungus_rep-seqs.qza
--o-classification fungus_taxonomy.qza
I get this error:
Traceback (most recent call last):
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 367, in load
archive.mount(path)
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 198, in mount
self.extract(filepath)
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 212, in extract
zf.extract(name, path=str(filepath.parent))
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/zipfile.py", line 1630, in extract
return self._extract_member(member, path, pwd)
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/zipfile.py", line 1702, in _extract_member
shutil.copyfileobj(source, target)
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/shutil.py", line 208, in copyfileobj
fdst_write(buf)
OSError: [Errno 28] No space left on deviceDuring handling of the above exception, another exception occurred:
OSError: [Errno 28] No space left on device
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/result.py", line 80, in load
archiver = archive.Archiver.load(filepath)
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 378, in load
cls._destroy_temp_path(archive.uuid)
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/archive/archiver.py", line 301, in _destroy_temp_path
cache.process_pool.remove(str(process_alias))
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/cache.py", line 1633, in remove
with self.cache.lock:
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/core/cache.py", line 292, in enter
self.flufl_lock.lock()
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/flufl/lock/_lockfile.py", line 328, in lock
self._write()
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/flufl/lock/_lockfile.py", line 493, in _write
fp.write(self._claimfile)
OSError: [Errno 28] No space left on deviceDuring handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/util.py", line 475, in _load_input_file
artifact = qiime2.sdk.Result.load(fp)
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/qiime2/sdk/result.py", line 84, in load
raise ValueError(f'There was not enough space left on '
ValueError: There was not enough space left on '/tmp' to extract the artifact 'unite_ver9_dynamic_25.07.2023-Q2-2023.7.qza'. (Try setting $TMPDIR to a directory with more space, or increasing the size of '/tmp')The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/click/type.py", line 116, in _convert_input
result, error = q2cli.util._load_input(value)
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/util.py", line 384, in _load_input
artifact, error = _load_input_file(fp)
File "/home/vzs95/miniconda3/envs/qiime2-2023.7/lib/python3.8/site-packages/q2cli/util.py", line 481, in _load_input_file
raise ValueError(
ValueError: It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'TaxonomicClassifier' and format 'TaxonomicClassiferTemporaryPickleDirFmt'There was a problem loading 'unite_ver9_dynamic_25.07.2023-Q2-2023.7.qza' as an artifact:
It looks like you have an Artifact but are missing the plugin(s) necessary to load it. Artifact has type 'TaxonomicClassifier' and format 'TaxonomicClassiferTemporaryPickleDirFmt'
See above for debug info.
Does anyone know how to fix the plugin issue? I can't find anything on what plugin I'd need to load my artifact. Any help would be appreciated.