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Running into an integer overflow error #41

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lilbluepenguin opened this issue Aug 15, 2024 · 0 comments
Open

Running into an integer overflow error #41

lilbluepenguin opened this issue Aug 15, 2024 · 0 comments

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@lilbluepenguin
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I am trying to use RIdeogram to generate a figure for the sugar pine genome using just the karyotype and labels (no heatmap), but... I keep running into the following error and warnings.

Error in if (min(diff(mydata)) >= myforce | tag == 3000) { :
missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In x[2] + x[3] : NAs produced by integer overflow
2: In x[2] + x[3] : NAs produced by integer overflow
3: In x[2] + x[3] : NAs produced by integer overflow
4: In x[2] + x[3] : NAs produced by integer overflow

I have a feeling the sugar pine genome might be too large? The total genome I'm working with is about 25 Gbp, the smallest full chromosome in the genome is 1.6 Gbp, but I get this error even when trying on two of the smallest "chromosomes" (as chr1 has already been split into halves because of limitations with other bioinformatics programs).
This is my input karyotype for this test on just the halves of chr1, as you can see the total length of chr1 is over 2.2 Gbp so I had to split it into two parts of roughly 1.1 Gbp. This is what the object chr1_karyotype outputs.

     Chr Start        End
1   chr1     0 1133725390
2 chr1.2     0 1133725370

this is what the top of my dataframe with the label information genes_chr1 looks like

  Type    Shape  Chr     Start       End  color
1    N      box chr1   5016826   5021996 FBFBF9
2   NL      box chr1  25892181  25895714 504A4B
3  TNL triangle chr1  93912698  93916141 FF5F1F
4   TN triangle chr1 294341875 294342639 FFE5B4
5  TNL triangle chr1 321372393 321377222 FF5F1F
6    N      box chr1 330926825 330927429 FBFBF9

and this is the command I am using just to check if the karyotype image is created without passing the labels as an argument, which it does

ideogram(karyotype = chr1_karyotype, output = "chromosome_1.svg")
convertSVG("chromosome_1.svg", device = "png", file= "chr1")

this is what chr1.png looks like:

image

but then when I try to add the label information with the following command I get the error I mentioned above

ideogram(karyotype = test_karyotype, label = genes_chr1, label_type = "marker", output="chr1_test.svg")

If this is indeed the error (genome being too large), do you know of a way I could work around this? If that is not the error, I would also greatly appreciate any help figuring out where I went wrong, Thank you.

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