kover : UnboundLocalError: local variable 'genome_ids' referenced before assignment

Question

[rania.assab]

Good afternoon,

To get the input of kover, I write this command

kover dataset create from-contigs --genomic-data ../../genome_paths_Amikacin.tsv --output ../../genome_pathMtb_output

and it tells me this:

UnboundLocalError: local variable 'genome_ids' referenced before assignment

Is there any explanation explaining why it tells me that the variable is referenced before assignment?

Thank you very much in advance

Best regards,

Answer 1

[Alexandre Drouin]

Hi Rania,

We resolved this via email, but I'm posting some info here in case someone else encounters the same issue.

Here are a few comments about the command line that was used:

• --output should be the path to the kover dataset that will be generated. I would recommend calling this ../../genome_pathMtb_output/dataset.kover (or something like that)

• You don’t provide any phenotype metadata (labels), which could be the cause of the problem. Labels must be provided in order for the algorithm to perform classification. You can find some example metadata files here: https://github.com/aldro61/kover2_paper/blob/master/data/mycobacterium%20tuberculosis/amikacin/metadata.tsv and a description of what’s in these files here: http://aldro61.github.io/kover/doc_input_formats.html#contigs.

• The full documentation for the “kover dataset create from-contigs” function can be found here: http://aldro61.github.io/kover/doc_dataset.html#from-contigs

and the conclusion was that the issue occurred since no phenotype metadata (labels) was provided.

[rania.assab]

Hi Alexandre,

Thank you very much :) (Sorry for the late) Yes exactly, I did not provide metadata labels

Thank you for all your rapid highlightings!

Best, Rania