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

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retrorna opened this issue Mar 8, 2024 · 0 comments
Open

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

retrorna opened this issue Mar 8, 2024 · 0 comments

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@retrorna
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retrorna commented Mar 8, 2024

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)?

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