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[动植物重测序] GCTA 分析GWAS报错求助

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    发表于 2019.1.31 15:56:48 | 显示全部楼层 |阅读模式

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    各位大神,我在用GCTA软件做GWAS分析时,在执行--mlma 时报错了,下面是报错信息:
    Reading PLINK FAM file from [4breeds_760.fam].
    760 individuals to be included from [4breeds_760.fam].
    Reading PLINK BIM file from [4breeds_760.bim].
    47466 SNPs to be included from [4breeds_760.bim].
    Reading PLINK BED file from [4breeds_760.bed] in SNP-major format ...
    Genotype data for 760 individuals and 47466 SNPs to be included from [4breeds_760.bed].
    Reading phenotypes from [phenotype.txt].
    There are 14 traits specified in the file [phenotype.txt].
    Trait #6 is included for analysis.
    Non-missing phenotypes of 711 individuals are included from [phenotype.txt].
    Reading quantitative covariates from [qcovar_pc12_bw0.txt].
    3 quantitative covariate(s) of 760 individuals read from [qcovar_pc12_bw0.txt].
    Reading discrete covariate(s) from [covar_sex.txt].
    1 discrete covariate(s) of 760 individuals are included from [covar_sex.txt].
    Reading IDs of the GRM from [4breeds_760.grm.id].
    760 IDs read from [4breeds_760.grm.id].
    Reading the GRM from [4breeds_760.grm.bin].
    GRM for 760 individuals are included from [4breeds_760.grm.bin].
    711 individuals are in common in these files.
    3 quantitative variable(s) included as covariate(s).
    1 discrete variable(s) included as covariate(s).

    Performing MLM association analyses (including the candidate SNP) ...

    Performing  REML analysis ... (Note: may take hours depending on sample size).
    711 observations, 5 fixed effect(s), and 2 variance component(s)(including residual variance).
    Calculating prior values of variance components by EM-REML ...
    Updated prior values: 285622 214855
    logL: -4844.86
    Running AI-REML algorithm ...
    Iter.        logL        V(G)        V(e)       
    1        -4636.87        0.93438        0.93438        (2 component(s) constrained)

    Error: analysis stopped because more than half of the variance components are constrained. The result would be unreliable.
    Please have a try to add the option --reml-no-constrain.


    然后我就按照他的提示加了--reml-no-constrain参数,再重新运行,发现
    Performing MLM association analyses (including the candidate SNP) ...

    Performing  REML analysis ... (Note: may take hours depending on sample size).
    711 observations, 5 fixed effect(s), and 2 variance component(s)(including residual variance).
    Calculating prior values of variance components by EM-REML ...
    Updated prior values: 285622 214855
    logL: -4844.86
    Running AI-REML algorithm ...
    Iter.        logL        V(G)        V(e)       
    1        -4636.87        -664915.15207        -53832.71160       

    Error: the information matrix is not invertible.



    我不太懂混合线性模型,我想问问,出现这种报错所涉及的问题是什么呢?谢谢大家啦!

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    发表于 2019.3.13 22:57:17 | 显示全部楼层

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