This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Running kover do not work

Good afternoon,

I am trying to run kover in my computer with the following command:

kover learn scm --dataset mypath/genome_paths.tsv --split 10

and it says:

IOError: Unable to open file (file signature not found)

Can you tell me where is my mistake?

Thank you very much in advance

Best regards, Rania Assab

kover
• 1,917 views • link
updated by Alexandre Drouin Alexandre Drouin • written by rania.assab • rania.assab

What is your current working directory, and where is mypath/genome_paths.tsv located in relation to your current working directory?

• 0 views • link
written by Kevin Blighe Kevin Blighe

In addition the file could also be corrupt. Check that as well.

• 0 views • link
written by GenoMax GenoMax

The file was the output of download-genomes.py a tsv file containing the genomes ids 'tab' fna file path

I checked them both and I do not know why it tells me that...

• 0 views • link
written by rania.assab • rania.assab

Here is the whole output message:

Traceback (most recent call last): File "/home/criuser/KOVER/kover/bin/kover", line 1192, in <module> CommandLineInterface()

File "/home/criuser/KOVER/kover/bin/kover", line 1150, in __init__

getattr(self, args.command)()

File "/home/criuser/KOVER/kover/bin/kover", line 1189, in learn

getattr(learning_tool, args.command)()

File "/home/criuser/KOVER/kover/bin/kover", line 510, in scm

dataset_kmer_count = pre_dataset.kmer_count

File "/home/criuser/.local/lib/python2.7/site-packages/kover/dataset/ds.py", line 78, in kmer_count

dataset = self.dataset_open()

File "/home/criuser/.local/lib/python2.7/site-packages/kover/utils.py", line 79, in _hdf5_open_no_chunk_cache

fid = h.h5f.open(filename, access_type)

File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper

File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper

File "h5py/h5f.pyx", line 88, in h5py.h5f.open

IOError: Unable to open file (file signature not found)

• 0 views • link
written by rania.assab • rania.assab

rania.assab : Looks like this file needs to be in HDF5 format? It does not seem to be.

• 0 views • link
written by GenoMax GenoMax

I finally found why thank you :) It is because my input is wrong yes

• 0 views • link
written by rania.assab • rania.assab

1 answer

There are two main modules to kover:

  1. Kover Dataset: takes care of packaging sequence data and phenotypes into a format on which machine learning analysis can be done efficiently (see: http://aldro61.github.io/kover/doc_dataset.html)
  2. Kover learn: takes care of the machine learning analysis, but requires data packaged as a "kover dataset" (http://aldro61.github.io/kover/doc_learning.html)

The problem here is that you were trying to use kover learn on something that wasn't a valid kover dataset.

• 0 views • link
written by Alexandre Drouin Alexandre Drouin

Log in to answer this question.

More posts like this