[Errno 38] Function not implemented - running qiime feature-classifier classify-consensus-vsearch

User Support
,
#1

Hi there.

I am trying to run qiime feature-classifier classify-consensus-vsearch but I am getting an error:
[Errno 38] Function not implemented:

The command I am using is:
qiime feature-classifier classify-consensus-vsearch
–i-query repseqs-clustering_dn97.qza
–i-reference-reads /media/hjunca/EXTERNAL2/Bio/qiime2/data_resources/ref-seqs132-99_FeatureDataSEQ.qza
–i-reference-taxonomy /media/hjunca/EXTERNAL2/Bio/qiime2/data_resources/ref-taxonomy132-99_FeatureDataTAX.qza
–p-perc-identity 0.97
–p-threads 10
–o-classification pollos_taxonomy_vsearch.qza
–p-strand plus

I’m not sure if this is the appropriate forum to ask this because maybe it is a problem with my python installation and not a Qiime2 issue… But the most common suggestion I have found is to create the directory /dev/shm which is already created… I actually haven found someone reporting this issue using qiime2.

Someone who can help me with this?

#2
#3

Hmm, it sounds like a problem with your conda environment. Did you install following the Native Install instructions? Or some other way?

Thanks! :t_rex: :qiime2:

#4
#5

Hi Matthew!,

Thank you for your answer. I haven't be able to fix it yet. Yes we did a Native Installation. We are using Ubuntu 16.04...

errno38.txt (3.2 KB)
We already run qiime vsearch uchime-denovo and qiime vsearch cluster-features-de-novo with no problem.

I have attached in a txt the complete line of the error, in case it is useful to understand it.

Thank you so much for your help.

#6

Hi again Matthew,
Actually, when I test my installation, I think everything looks ok…

(qiime2-2018.4) [email protected]:~$ qiime --help
Usage: qiime [OPTIONS] COMMAND [ARGS]…

QIIME 2 command-line interface (q2cli)

To get help with QIIME 2, visit https://qiime2.org.

To enable tab completion in Bash, run the following command or add it to
your .bashrc/.bash_profile:

  source tab-qiime

To enable tab completion in ZSH, run the following commands or add them to
your .zshrc:

  autoload bashcompinit && bashcompinit && source tab-qiime

Options:
–version Show the version and exit.
–help Show this message and exit.

Commands:
info Display information about current deployment.
tools Tools for working with QIIME 2 files.
dev Utilities for developers and advanced users.
alignment Plugin for generating and manipulating alignments.
composition Plugin for compositional data analysis.
cutadapt Plugin for removing adapter sequences, primers, and
other unwanted sequence from sequence data.
dada2 Plugin for sequence quality control with DADA2.
deblur Plugin for sequence quality control with Deblur.
demux Plugin for demultiplexing & viewing sequence quality.
diversity Plugin for exploring community diversity.
emperor Plugin for ordination plotting with Emperor.
feature-classifier Plugin for taxonomic classification.
feature-table Plugin for working with sample by feature tables.
gneiss Plugin for building compositional models.
longitudinal Plugin for paired sample and time series analyses.
metadata Plugin for working with Metadata.
phylogeny Plugin for generating and manipulating phylogenies.
quality-control Plugin for quality control of feature and sequence data.
quality-filter Plugin for PHRED-based filtering and trimming.
sample-classifier Plugin for machine learning prediction of sample
metadata.
taxa Plugin for working with feature taxonomy annotations.
vsearch Plugin for clustering and dereplicating with vsearch.

#7
#8

Hmm!

It looks like some of your reference files might be on an external drive / network drive. Maybe you could try copying them locally to the drive you are working with your data on and try running the command again?

Keep us posted! :t_rex: :qiime2:

#9
#10

Hi Matthew!

You were right, I think this is working now!!! Thank you so much!!!

1 Like
#11

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