Dear All,

I'm new to PopGenome packages and I tried to use it for genetic diversity calculations according to its examples in the manual. However, it produced an error and I don't know how to fix it even after reading the manual. Is there any advice to figure it out or fix it? Thanks. Below is my code and some results:

PopGenome::VCF_split_into_scaffolds("cmVCF_jt_snp_flt2_flt6.vcf","scaffoldVCFs")
allgenomes <- PopGenome::readData("scaffoldVCFs",format="VCF")
get.individuals(allgenomes)[[1]]
pop1 <- c("MSub10")
pop2 <- c("S11")
pop3 <- c("S12")
pop4 <- c("S13")
.....
pop11 <- c("S6")
pop12 <- c("mergeSub")
allgenomes_pop <- PopGenome::set.populations(allgenomes, list(pop1,pop2,pop3,pop4,pop5,pop6,pop7,pop8,pop9,pop10,pop11,pop12))
allgenomes_pop_div <- PopGenome::diversity.stats(allgenomes_pop)

The result of get.individuals(allgenomes)[[1]]: [1] "MSub10" "S11" "S12" "S13" "S18" "S20"
[7] "S29" "S30" "S32" "S38" "S6" "mergeSub" The result of allgenomes_pop@populations: [[1]] [1] "MSub10"

[[2]] [1] "S11"

[[3]] [1] "S12"

[[4]] [1] "S13"

[[5]] [1] "S18"

[[6]] [1] "S20"

[[7]] [1] "S29"

[[8]] [1] "S30"

[[9]] [1] "S32"

[[10]] [1] "S38"

[[11]] [1] "S6"

[[12]] [1] "mergeSub"

The error produced by PopGenome::diversity.stats(allgenomes_pop):

Error: $ operator is invalid for atomic vectors

I've tried "diversity.stats()" without setting populations, it proceeded without error messages. I've tried "diversity.stats.betwwen()" with setting populations, it proceeded without error messages. And I used PopGenome::, since there are some package mask warnings, when I load the package PopGenome. Below are warnings:

Loading required package: ff Loading required package: bit

Attaching package: ‘bit’

The following object is masked from ‘package:base’:

xor

Attaching package ff - getOption("fftempdir")=="/tmp/RtmpZf0qhS/ff"

• getOption("ffextension")=="ff"

• getOption("ffdrop")==TRUE

• getOption("fffinonexit")==TRUE

• getOption("ffpagesize")==65536

• getOption("ffcaching")=="mmnoflush" -- consider "ffeachflush" if your system stalls on large writes

• getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

• getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system

Attaching package: ‘ff’

The following objects are masked from ‘package:utils’:

write.csv, write.csv2

The following objects are masked from ‘package:base’:

is.factor, is.ordered

In addition, when I tried to set populations in R from bash, the cursor just stuck at the 100 % position and didn't return. And I can only type return by myself. Below is the result: allgenomes_pop <- PopGenome::set.populations(allgenomes,list(pop1, pop2, pop3, pop4, pop5, pop6, pop7, pop8, pop9, pop10, pop11, pop12))

| : | : | 100 %

|====================================================>cursor

However, the cursor didn't got stuck when I tried it on R software in my computer.