Error: $ operator is invalid for atomic vectors

[jhurst5]

Hi Xiaolei,

I am getting the following error

[1] "Current loop: 2 out of maximum of 10"
[1] "Optimizing Pseudo QTNs..."
Error: $ operator is invalid for atomic vectors
In addition: Warning messages:
1: In ID.GP/bin.size :
 longer object length is not a multiple of shorter object length
2: In if (!is.na(inclosure.size)) { :
  the condition has length > 1 and only the first element will be used
3: In parallel::mclapply(1:m, seqQTN.optimize.parallel, mc.cores = ncpus) :
  all scheduled cores encountered errors in user code
Execution halted

I have tried changing minor things, but cannot figure out what the issue is. Any help would be appreciated.

[jhurst5]

Here is the input:

genotype = attach.big.matrix("/path/mvp4.hmp.geno.desc")

phenotype = read.table("/path/mvp4.hmp.phe", head=TRUE)

map = read.table("/path/mvp4.hmp.map", head=TRUE)

myMVP = MVP(
phe=phenotype,
geno=genotype,
map=map,
nPC.FarmCPU=3,
perc = 1,
priority="speed",
ncpus=5,
vc.method="EMMA",
maxLoop=10,
method.bin="EMMA",
threshold=0.05,
method="FarmCPU"
)

[jhurst5]

In addition, when I set Max Loop to 1, it runs to completion

[XiaoleiLiuBio]

Could you please check if there are non numeric records in second and third column in map file?

[jhurst5]

No, there are no non-numeric records.

[XiaoleiLiuBio]

Please send me (xiaoleiliu@mail.hzau.edu.cn) a demo data that can repeat the error, I will test and debug it. Thank you.