Error in strsplit(.peak_sizes[, "structure"], "") : non-character argumen

[AlcaArctica]

Hi and thank you for this great tool! I am trying to use smudgeplot for hifi data of a large amphibian genome. I am executing:

# Run FastK to create a k-mer database
/u/luelze/sw/FASTK-1.1.0/FastK -P/ptmp/luelze/ptmp -v -t72 -k31 -M16 -T4 data/*.fastq.gz -Ndata/FastK_Table

# Find all k-mer pairs in the dataset using hetmer module
/raven/u/luelze/sw/smudgeplot/exec/smudgeplot.py hetmers -L 12 -t 72 -o data/kmerpairs --verbose data/FastK_Table

# Use the .smu file to infer ploidy and create smudgeplot
/raven/u/luelze/sw/smudgeplot/exec/smudgeplot.py all -o data/trial_run data/kmerpairs_text.smu

However the last step all produces the following error:

Calling: smudgeplot_plot.R -i "data/trial_run_masked_errors_smu.txt" -s "data/trial_run_smudge_sizes.txt" -n 9.75 -o "data/trial_run"  -col_ramp "viridis"
Error in strsplit(.peak_sizes[, "structure"], "") : 
  non-character argument
Calls: plot_expected_haplotype_structure -> strsplit
Execution halted

and the output plots are empty. I am not sure what is going on. The same happens with a different data set (hifi data of a bird species). For other species I have managed to run smudgeplot successfully. Both the bird and the amphibian are diploid.

I have attached all relevant files and would be very happy if you could help me to debug it! Thank you very much!

I am using smudgeplot v0.4.0dev and FASTK-1.1.0.

I will try to attach the data of the bird as it is smaller: https://drive.google.com/file/d/1uheak3pEi4KvQXYA8OsDQMVuQVQw6AIY/view?usp=share_link

It looks similar to this issue: https://github.com/KamilSJaron/smudgeplot/issues/184

But I do not think the problem is sequencing depth. I got a great assembly of the bird with a coverage per haplotig of 20x.

Thank you very much for your help