Error in if (acceptance.ratio >= 0)

[Penglanhui]

Hi Joel,

I ran the program on the example dataset using the code suggested in the help menu.

run.startmrca(vcf.file="FIN_chr2_pos136608646.vcf.gz",

• rec.file="decode_recmap_sexaveraged.txt",
• sample.ids="sample_ids.txt",
• refsample.ids="sample_ids.txt",
• mut.rate=1.6e-8,
• nsel=50,
• nanc=20,
• chain.length=20,
• nanc.post=10,
• pos=136608646,
• sel.allele=1)

The output is shown below:

[1] "Getting data from the vcf."
[1] "Removing variable sites with duplicated ID in the vcf (only the first sites are kept)."
[1] "Selected allele carrier IDs are specified."
Read 105 items
[1] "Reference panel IDs are specified."
[1] "Reference panel is the same as the carrier panel."
|======================================================================| 100%
[1] "Estimating the ancestral haplotype."
[1] "Getting the recombination map."
|======================================================================| 100%
[1] "Initializing the MCMC."
[1] "Starting the MCMC."
| | 0%Error in if (acceptance.ratio >= 0) { :
missing value where TRUE/FALSE needed

Is there any idea?
Thanks!

Lanhui

[salonso65]

I have the same problem. Could you solve it?

[Tanlizhicau]

hey guys ,is your operating system Windows？try turn to Linux or OS,the package will work on.

[Penglanhui]

I think it's about the environment settings. I was using Linux, so it probably was not about the operating system.
But I solved it by using another server, not knowing why.