Eigensoft-smartpca分析PCA报错：warning (mapfile): bad chrom: Segmentation fault

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问题
解决

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 usedwarning (mapfile): bad chrom: 100100:181601816 warning (mapfile): bad chrom: 101101:138801388 warning (mapfile): bad chrom: 101101:192201922 warning (mapfile): bad chrom: 102102:128601286 warning (mapfile): bad chrom: 103103:8670867 warning (mapfile): bad chrom: 104104:1490149 warning (mapfile): bad chrom: 105105:153201532 warning (mapfile): bad chrom: 106106:120101201 warning (mapfile): bad chrom: 107107:111301113 warning (mapfile): bad chrom: 108108:2550255 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