OmicShare Class 基迪奥生物信息在线课堂

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资料

gcta64 --make-grm --out snp.gcta --bfile lecture09cc.maf0.05.hwe6.miss0.2.ind0.2 --autosome-num 22

出现错误

*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.26.0
* (C) 2010-2016, The University of Queensland
* MIT License
* Please report bugs to: Jian Yang <jian.yang@uq.edu.au>
*******************************************************************
Analysis started: Thu Dec 20 15:59:50 2018

Options:
--make-grm
--out snp.gcta
--bfile lecture09cc.maf0.05.hwe6.miss0.2.ind0.2
--autosome-num 22

Note: This is a multi-thread program. You could specify the number of threads by the --thread-num option to speed up the computation if there are multiple processors in your machine.

Reading PLINK FAM file from [lecture09cc.maf0.05.hwe6.miss0.2.ind0.2.fam].
600 individuals to be included from [lecture09cc.maf0.05.hwe6.miss0.2.ind0.2.fam].
Reading PLINK BIM file from [lecture09cc.maf0.05.hwe6.miss0.2.ind0.2.bim].
19638 SNPs to be included from [lecture09cc.maf0.05.hwe6.miss0.2.ind0.2.bim].
Reading PLINK BED file from [lecture09cc.maf0.05.hwe6.miss0.2.ind0.2.bed] in SNP-major format ...
Genotype data for 600 individuals and 19638 SNPs to be included from [lecture09cc.maf0.05.hwe6.miss0.2.ind0.2.bed].

Error: this option is for the autosomal SNPs only. Please check the option --autosome.

Analysis finished: Thu Dec 20 15:59:51 2018
Computational time: 0:0:1

如何解决????

1809天前

xiek 回复 ljljlxh12 ：

我的数据应该是 --autosome-num 19

#1 1788天前回复

ljljlxh12

用的数据是老师提供的

1809天前

ljljlxh12

谢谢老师

1753天前

Ali_19

Fatal Error : Expected a Chromosome in the form of an integer from 0-26 in file [fastlmm_in.tped] near line 277594:1. Found [91]

老师，请问这个错误是什么意思？

1748天前

Ali_19

老师，我明白是怎么回事了，是不是只要替换成0-26之内的数字或者X，Y之类的就可以了。FastLMM软件不接受这些字符以外的染色体序号是不是？

#1 1748天前回复

xiek 回复 Ali\%19 ：

有参数可以接受超过这个范围的，-MaxChromosomeValue

#2 1614天前回复

专抢小孩棒棒糖

plink --bfile lecture09.case.control --maf 0.05 --hwe 1e-6 --geno 0.2 --mind 0.2 --make-bed --out lecture09cc.maf0.05.hwe6.miss0.2.ind0.2
plink: unknown option "--bfile"
plink: unknown option "--maf"

这个是怎么回事呢？

1524天前