The problems encountered when using the command “smudgeplot.py all”

[liuweiming1]

I encountered some issues after using the command “smudgeplot.py all -o ./trial_run ./kmerpairs_text.smu -ylim 70”.

Error in strsplit(.peak_sizes[, "structure"], "") : 
  non-character argument
Calls: plot_expected_haplotype_structure -> strsplit
Execution halted

Why did this problem occur?
And some of the files generated in this step are problematic.

trial_run_smudge.sizes.txt is an empty file. And the file trial_run_smudgeplot.pdf opens to look like the following image.

So I reduced the value of the L parameter in the previous step: smudgeplot.py hetmers -L 5 -t 4 -o ./data/kmerpairs --verbose ./data/Scer.ktab.
After I reduced the value of the L parameter in the previous step, I continued to use the command smudgeplot.py all -o ./trial_run ./kmerpairs_text.smu -ylim 70, but the same error still occurred

So what should I do now?

[KamilSJaron]

Hi @liuweiming1 , some of the images you intended to upload are not there... would you like to try that again? How does you .smu file looks like? Could you perhaps upload that one here too?

It is hard to debug without these details.

[liuweiming1]

Hi @liuweiming1 , some of the images you intended to upload are not there... would you like to try that again? How does you .smu file looks like? Could you perhaps upload that one here too?

It is hard to debug without these details.

Sure, here is the error message：

And here is the screenshot of the .smu file：

[liuweiming1]

Hi @liuweiming1 , some of the images you intended to upload are not there... would you like to try that again? How does you .smu file looks like? Could you perhaps upload that one here too?

It is hard to debug without these details.

Here is also a screenshot of the trial_run_smudgeplot.pdf:

I hope you can help me figure out what went wrong. Thank you!

[KamilSJaron]

Hi @liuweiming1, I see what's probably happening here.

I think you just simply don't have an adequate sequencing depth. Did you make a k-mer histogram too? You should plot it and figure out if you see distinct peaks.

[KamilSJaron]

I updated https://github.com/KamilSJaron/smudgeplot/wiki/everything-about-input-data with the information about needed coverage and what patterns to expect when not met....

[liuweiming1]

I updated https://github.com/KamilSJaron/smudgeplot/wiki/everything-about-input-data with the information about needed coverage and what patterns to expect when not met....
I replaced the data with HiFi data, ran it again, and generated the graph below. I am certain that my species is an allotetraploid, and the final result also shows AABB at 75%. But why does the graph look like this?

[KamilSJaron]

Hi @liuweiming1 I am always happy to help, but you got to give me more than this...

1. You really need to look at / post here the histogram as well as the smudgeplot (See https://github.com/KamilSJaron/smudgeplot/wiki/joint-interpretation-of-smudgeplot-and-GenomeScope)
2. If you want to some reasonable insights, you also need to give me a bit about the biology of your species - what it is, why you expect allotetraploidy, exp. genome size, what else you know that is relevant...
3. I would really appreciate a bit kinder tone, I do this in my free time because there is no way how can I squeeze pro bono help to the global community within my working hours. I don't need much, hi and thank you when I respond with something useful would do...