[Errno 38] Function not implemented using feature-classifier but I need and extra disk

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) [email protected]:/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) [email protected]:~$ 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…

Hi there @Marcela_Villegas - sorry about the late reply.

It looks like this problem isn’t solved — the error you pasted below still says the same thing:

“[Errno 38] Function not implemented: ‘/media/hjunca/EXTERNAL2/tmp/tmp.FKiJ4m1XRH/qiime2-provenance-n3foef5i/artifacts/57f511e4-2855-4755-bbe1-412b23640110’”)]

Maybe try setting your TMPDIR to this external drive AND move your data to that drive, as well?

Hi @thermokarst Thank you for your help…
This is how I’ve been tried: My TMPDIR and my data are in the same drive. But the same error is occurring.
I am thinking on reinstall Qiime2 and conda env.

1 Like

I think that sounds like a good idea. Something is certainly strange with this particular computing environment, but I am not sure what.

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