Skip to content

Error with k-mer sizes other than 5 when executing in terminal  #21

@retrorna

Description

@retrorna

Hi,

I tried running this with k-mer length set to 3, 4 or 6 (these ones I tried) and got the following error.

INFO [2024-03-08 10:00:42] Started
WARN [2024-03-08 10:00:42] No output filename provided. Generating automatic output name in current directory. You can specify an output TSV filename with --output

INFO [2024-03-08 10:00:42] Logging level             : INFO
INFO [2024-03-08 10:00:42] Number of cores           : 4

INFO [2024-03-08 10:00:42] Input FASTA file          : /fasta
INFO [2024-03-08 10:00:42] k-mer length              : 6
INFO [2024-03-08 10:00:42] lambda                    : 1
INFO [2024-03-08 10:00:42] Scaling function          : exp(-1*x)
INFO [2024-03-08 10:00:42] Multivalency window size  : 123
INFO [2024-03-08 10:00:42] Smoothing window size     : 123
INFO [2024-03-08 10:00:42] Output TSV filename       : fasta_6_123_123.multivalency.tsv.gz

INFO [2024-03-08 10:00:42] Building scoring matrices
Error in value[[3L]](cond) : `glue` failed in `formatter_glue` on:

  chr "Scaled Hamming: {0:5} = {round(scaled.v, 3)}" 

Raw error message:

 Variables must be length 1 or 7 

Please consider using another `log_formatter` or `skip_formatter` on strings with curly braces.
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

When ran with k-mer length set to 5 it runs successfully.

And a feature request: could wildcard nucleotides (for example R being either A or G) be somehow regarded as such when calculating multivalency scores (meaning the score is calculated for all versions of the k-mers)?

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions