GWAS中gapit分析没有结果,命令行输入与屏幕输出如下

Rscript ./gapit_gwas.r -i ../00.filter/hapmap.txt.gz -t ../trait.tsv  -m GLM  -n hd.GLM.GWAS.Results 

WARNING: ignoring environment value of R_HOME

--> Q&A for bioinformatics, please visit the website: https://www.omicsclass.com/

--> R beginners ? I suggest your  learning  R language: https://study.omicsclass.com/index

Loading required package: BiocGenerics


Attaching package: ‘BiocGenerics’


The following objects are masked from ‘package:stats’:


    IQR, mad, sd, var, xtabs


The following objects are masked from ‘package:base’:


    anyDuplicated, aperm, append, as.data.frame, basename, cbind,

    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,

    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,

    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,

    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,

    table, tapply, union, unique, unsplit, which.max, which.min


Loading required package: Biobase

Welcome to Bioconductor


    Vignettes contain introductory material; view with

    'browseVignettes()'. To cite Bioconductor, see

    'citation("Biobase")', and for packages 'citation("pkgname")'.



Attaching package: ‘gplots’


The following object is masked from ‘package:multtest’:


    wapply


The following object is masked from ‘package:stats’:


    lowess


Loading required package: combinat


Attaching package: ‘combinat’


The following object is masked from ‘package:utils’:


    combn


Loading required package: gdata

Registered S3 method overwritten by 'gdata':

  method         from

  reorder.factor gplots


Attaching package: ‘gdata’


The following object is masked from ‘package:gplots’:


    reorder.factor


The following object is masked from ‘package:Biobase’:


    combine


The following object is masked from ‘package:BiocGenerics’:


    combine


The following object is masked from ‘package:stats’:


    nobs


The following object is masked from ‘package:utils’:


    object.size


The following object is masked from ‘package:base’:


    startsWith


Loading required package: gtools

Loading required package: MASS

Loading required package: mvtnorm



NOTE: THIS PACKAGE IS NOW OBSOLETE.




  The R-Genetics project has developed an set of enhanced genetics


  packages to replace 'genetics'. Please visit the project homepage


  at http://rgenetics.org for informtion.





Attaching package: ‘genetics’


The following objects are masked from ‘package:BiocGenerics’:


    %in%, order


The following objects are masked from ‘package:base’:


    %in%, as.factor, order


Loading required package: LDheatmap

Loading required package: ape

Loading required package: grid

Loading required package: bigmemory

Loading required package: EMMREML

Loading required package: Matrix

Loading required package: lme4

Killed


请先 登录 后评论

1 个回答

omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

最后 killed 内存不够导致系统杀死任务,如果用的docker可以看看这里设置容器内存:https://www.omicsclass.com/article/1413

请先 登录 后评论