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"