课程资料也相应更新了：https://www.omicsclass.com/article/2286，所以你的脚本也需要重新下载更新才行；不然你还是用之前版本的镜像，v1.2 

因为latest现在就是2.0 所以很快下载完成；

老师，我在集群上重新下载了pop-evol-gwas.sh, 重新在课上的公众号下载了脚本，然后再运行GAPIT关联分析，但是还是有问题。Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 

  line 1 did not have 3 elements

Calls: read.table -> scan

In addition: Warning messages:

1: In read.table(opt$input, head = FALSE, comment.char = "", stringsAsFactors = F) :

  line 1 appears to contain embedded nulls

2: In read.table(opt$input, head = FALSE, comment.char = "", stringsAsFactors = F) :

  line 2 appears to contain embedded nulls

3: In read.table(opt$input, head = FALSE, comment.char = "", stringsAsFactors = F) :

  line 5 appears to contain embedded nulls

Execution halted

这是我的命令：module load base

module load anaconda3

workdir=/public/home/majieyu/perl5/lpgwas/my_gwas

refdir=$workdir/ref

datadir=$workdir/data

scriptdir=$workdir/scripts

tmpdir=$workdir/tmp

GFF=$refdir/Lp.gff3

REF=$refdir/Lp.fasta

FAI=$refdir/Lp.fasta.fai

kinship=$workdir/07.gwas_tassel/kinship.txt

structure=$workdir/07.gwas_tassel/pca1.txt

vcf=$workdir/00.filter/clean.vcf

hmp=$workdir/00.filter/clean.hapmap.txt.zip

/public/software/singularity/bin/singularity exec /public/software/singularity/docker-images/pop-evol-gwas.sif \

bash -c "Rscript $scriptdir/gapit_gwas.r -i $hmp -t $workdir/05.trait/HIS-LWC.txt  -m GLM -n hd.GLM.GWAS.HIS-LWCResults"