unable to load shared object '/home/wanghj/R/x86_64-pc-linux-gnu-library/4.2/00LOCK-igraph/00new/igraph/libs/igraph.so': libglpk.so.36: cannot open shared object file: No such file or directory
如上面的报错,这个时候最简单的办法是通过locate查看是否存在链接库(linux里)...
...eles 2 |gzip - > all.clean.vcf.gz
结果是After filtering, kept 0 out of a possible 118111 Sites（中间很多Warning），于是把参数全部拆开一次只过滤一个参数，发现除了--min-alleles 2 --max-alleles 2，可以过滤成功：kept 106816 out of a possible 118111 Sites之...
... rng.seed = 362436069)
{
rng.state <- NULL
if (exists(".Random.seed")) {
rng.state <- .Random.seed
}
set.seed(rng.seed)
x <- data
p <- nrow(x)
col.nas <- drop(rep(1, p) %*% is.na(x)) #matrix multiplication #count NA number in eac...
筛选出的deg的基因emsembl id无法进行转成entrezid，说不存在这些id
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.
Calls: bitr
Execution halted
...组的时候需要用到Progressive Cactus
参考文章：Dense sampling of bird diversity increases power of comparative genomic
下载：
软件github：https://github.com/ComparativeGenomicsToolkit/cactus
选择的是Pre-compiled Binaries Linux Tarball这个版本：
wget https://github.com...
...s → docker scout quickview omicsclass/gene-family:v1.0.1
Error response from daemon: pull access denied for omicsclass/gene-family, repository does not exist or may require 'docker login': denied: requested access to the resource is denied
PS C:\Users\Administrator> docker search omicsclass
...
...放了所有样品的集合，但是跑出来是如下这样
the Number of subPop samples[found in VCF] is 0
sub Group Population szie istoo small, SubGroup sample size: 0
##begin pair-wise R^2 cal. after filter Remain SNP Number : 0
#% number bin is11%......-->100%........
... generated? (BLUE = best linear unbiased estimate) (Default: false)
-saveToFile <true | false> : Should the results be saved to a file rather than stored in memory? It true, the results will be written to a file as each SNP is analyzed in order to reduce memory requirementsand the results wil...