Hi there!
I am stuck in the taxonomy assignment step... @thermokarst already given me an explanation about [Errno 38] Function not implemented, but I have not found the solution.
I have a machine with two different disks, the reason of this is because there is not enough space in the native disk of my server, so we are using a second disk with plenty of space:
(qiime2-2018.4) hjunca@Modeling2:/media/hjunca/EXTERNAL2/MICROBIOMAS/TEMP$ df -h
S.ficheros Tamaño Usados Disp Uso% Montado en
udev 7,8G 4,0K 7,8G 1% /dev
tmpfs 1,6G 1000K 1,6G 1% /run
/dev/sda6 185G 169G 6,8G 97% /
none 4,0K 0 4,0K 0% /sys/fs/cgroup
none 5,0M 0 5,0M 0% /run/lock
none 7,9G 596K 7,9G 1% /run/shm
none 100M 32K 100M 1% /run/user
/dev/sda2 96M 29M 68M 30% /boot/efi
/dev/sdb1 932G 11G 921G 2% /media/hjunca/EXTERNAL2
When I first run some of these two commands:
qiime feature-classifier fit-classifier-naive-bayes \
--i-reference-reads ref-seqs132-99_V1V2.qza \
--i-reference-taxonomy ref-taxonomy132-99_FeatureDataTAX.qza \
--o-classifier classifier132-99_V1V2.qza
qiime feature-classifier classify-consensus-vsearch \
--i-query repseqs-clustering_dn97.qza \
--i-reference-reads ref-seqs132-99_FeatureDataSEQ.qza \
--i-reference-taxonomy ref-taxonomy132-99_FeatureDataTAX.qza \
--p-perc-identity 0.97 \
--p-threads 10 \
--o-classification pollos_taxonomy_vsearch.qza \
--p-strand plus
I got the following error:
Plugin error from feature-classifier:
[Errno 28] No space left on device
So I searched where the directory of temporary files was located, and I got no results (a blank space):
(qiime2-2018.4) hjunca@Modeling2:~$ echo $TMPDIR
So I set my TMPDIR to /media/hjunca/EXTERNAL2 which has plenty of space (932G) and tried to re-run qiime feature-classifier fit-classifier-naive-bayes and qiime feature-classifier classify-consensus-vsearch and now the error is:
Traceback (most recent call last):
File "/home/hjunca/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/q2cli/commands.py", line 274, in __call__
results = action(**arguments)
File "<decorator-gen-274>", line 2, in fit_classifier_naive_bayes
File "/home/hjunca/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/sdk/action.py", line 211, in bound_callable
provenance.add_input(name, artifact)
File "/home/hjunca/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/core/archive/provenance.py", line 406, in add_input
self.inputs[name] = self.add_ancestor(input)
File "/home/hjunca/miniconda2/envs/qiime2-2018.4/lib/python3.5/site-packages/qiime2/core/archive/provenance.py", line 159, in add_ancestor
ignore=shutil.ignore_patterns(self.ANCESTOR_DIR + '*'))
File "/home/hjunca/miniconda2/envs/qiime2-2018.4/lib/python3.5/shutil.py", line 359, in copytree
raise Error(errors)
shutil.Error: [('/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-archive-eevvh09c/57f511e4-2855-4755-bbe1-412b23640110/provenance/action/action.yaml', '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/action/action.yaml', "[Errno 38] Function not implemented: '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/action/action.yaml'"), ('/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-archive-eevvh09c/57f511e4-2855-4755-bbe1-412b23640110/provenance/action', '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/action', "[Errno 38] Function not implemented: '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/action'"), ('/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-archive-eevvh09c/57f511e4-2855-4755-bbe1-412b23640110/provenance/metadata.yaml', '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/metadata.yaml', "[Errno 38] Function not implemented: '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/metadata.yaml'"), ('/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-archive-eevvh09c/57f511e4-2855-4755-bbe1-412b23640110/provenance/citations.bib', '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/citations.bib', "[Errno 38] Function not implemented: '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/citations.bib'"), ('/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-archive-eevvh09c/57f511e4-2855-4755-bbe1-412b23640110/provenance/VERSION', '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/VERSION', "[Errno 38] Function not implemented: '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110/VERSION'"), ('/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-archive-eevvh09c/57f511e4-2855-4755-bbe1-412b23640110/provenance', '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110', "[Errno 38] Function not implemented: '/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110'")]
So if I am understanding well, the problem is that I have my database files, my output directory and my temporally files directory in a different disk in where I did the installation of Qiime2... Is that right?? What should I do? Should I re install Qiime 2 over the EXTERNAL2 disk?
I already run qiime vsearch uchime-denovo, qiime vsearch cluster-features-de-novo in this machine with no problem.
My apologies for taking you busy with this, but I don't know what to do…