使用了pop-evol-gwas2.0,还是报错,但是我安装的时候这个2.0特别快,一下就好了。

attachments-2024-01-eaabmRJG65af35ce30ffa.jpg

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2 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

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;

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马杰宇

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"

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