问题

一直以来用Eigensoft的smartpca来做群体遗传的PCA分析很顺畅，结果也比较靠谱。

但今天报错如下：

$ ~/miniconda3/bin/smartpca -p smartpca.par
parameter file: smartpca.par
### THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
genotypename: plink.ped
snpname: plink.pedsnp
indivname: plink.pedind
evecoutname: pca.vec
evaloutname: pca.val
numoutlieriter: 0
numchrom: 1000000
## smartpca version: 16000
norm used

warning (mapfile): bad chrom: 100   100:1816    0   1816
warning (mapfile): bad chrom: 101   101:1388    0   1388
warning (mapfile): bad chrom: 101   101:1922    0   1922
warning (mapfile): bad chrom: 102   102:1286    0   1286
warning (mapfile): bad chrom: 103   103:867 0   867
warning (mapfile): bad chrom: 104   104:149 0   149
warning (mapfile): bad chrom: 105   105:1532    0   1532
warning (mapfile): bad chrom: 106   106:1201    0   1201
warning (mapfile): bad chrom: 107   107:1113    0   1113
warning (mapfile): bad chrom: 108   108:255 0   255
Segmentation fault

这个原因有可能是染色体号为0导致。smartpca中 ，0意味着染色体编号信息缺失。

检查我的map文件中第一列（染色体号），从1开始，并没有为0。以前用带chr或scaffold开头的染色体数据做过，也没有报错。

解决

在Google group上找到了原因。

I have got Smartpca within EIGENSOFT (6.0.1) to work without converting with convertf - it will take map/ped directly.  I have madified the output map/ped that stacks outputs.

EIGENSOFT and PLINK don't with thousands of chromosomes/contigs well - so I would suggest removing that info from the map file - replace the first column with all '1' for example.  I do have some chromosome info so I have chromosomes 1-37 for assigned loci and I used for '40' for unassigned loci.  I dont think smartpca likes a zero in the frist column of the map file.

example map file: 

[https://github.com/rwaples/chum_populations/blob/master/results/batch_4/EIGENSOFT/complete.codom.subsample.map](https://github.com/rwaples/chum_populations/blob/master/results/batch_4/EIGENSOFT/complete.codom.subsample.map)

ped file - I have the phenotype (col 6) set to missing (-9) and smartpca complains about it - but it works.  

example ped file:

[https://github.com/rwaples/chum_populations/blob/master/results/batch_4/EIGENSOFT/complete.codom.subsample.ped](https://github.com/rwaples/chum_populations/blob/master/results/batch_4/EIGENSOFT/complete.codom.subsample.ped)

example parfile:

[https://github.com/rwaples/chum_populations/blob/master/results/batch_4/EIGENSOFT/complete.codom.subsample.parfile](https://github.com/rwaples/chum_populations/blob/master/results/batch_4/EIGENSOFT/complete.codom.subsample.parfile) 

-Ryan

https://groups.google.com/g/stacks-users/c/rkN9Q5G6hXg

可以看到smartpca并不支持上千条的scaffold/contig（查看了下我的数据，有3000多contigs），而在做PCA分析时，染色体号并不影响最终结果。因此可将很碎的contig统一一个染色体号。

sed 's/contig[0-9]*/20/g' map.vcf

最终得到所有材料PCA结果。

https://www.jianshu.com/p/bdf1bc116127