plot err

[zskey-zn]

I follow (https://github.com/BGAcademy23/smudgeplot) to run my species，but smudeplot send Error:

Running smudgeplot v0.3.0dev
Task: plot
Calling: smudgeplot_plot.R -i "LY_k21_pairs_text.smu" -o "LY_k21_smudgeplot" -col_ramp "viridis"

######################
## INPUT PROCESSING ##
######################

#############
## SUMMARY ##
#############
detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 	35
detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 	30
detecting two smudges at the same positions, not enough data for this number of bins lowering number of bins to 	25
!! Warning, your coverage filter on the lower end (L = 	24	) is higher than half of the 1n coverage estimate ( 1n / 2 = 	18.4
If the real 1n coverage is half of your estimate you would not picked it up due to the filtering.
If you have sufficient coverage, consider reruning the analysis with lower L (something like (1n / 2) - 5)
One good way for verificaiton would be to compare it to GenomeScope estimate of haploid coverage

##########
## PLOT ##
##########
Error in as.graphicsAnnot(legend) : 
  argument "legend" is missing, with no default
Calls: plot_histograms -> legend -> as.graphicsAnnot
Execution halted

Done!

and result seems strange.

my code and output are as follows

FastK -v -t4 -k21 -M16 -T16  .../LY_dedup.[12].fq  -NLY -Ptmp
Histex -G LY > LY_k21.hist
smudgeplot.py hetmers -L 24 -t 4 --verbose -o LY_k21_pairs LY.ktab
smudgeplot.py plot -o LY_k21_smudgeplot LY_k21_pairs_text.smu

LY.zip

How can I fix this bug?

[KamilSJaron]

Hi @zskey-zn , thanks tons for trying out the new version. We still need to catch all the small things and this indeed looks like a bug of sorts. And thanks even more for attaching the dataset, that will allow me to try to debug it.

I will try to look into your data sometime soon and look what is causing it. A have a few more tasks for this week so please bear with me.

I recon octoploidy would come as a suprise?

K

[zskey-zn]

Thanks to reply ! The octaploid is as expected，do I need to provide *.ktab as well?

[KamilSJaron]

It should be fine as is! Thanks.