hewm2008 / vcf2pcacluster Goto Github PK

hi,When my install the software, there is a error. The error as follows:
configure: error: cannot find sources (src/VCF2PCACluster.cpp) in . or ..
Can you help me?

Can't find the [gnuplot] at $PATH or $BinDir
you can export it to get more Fig
Loading required package: gplots

Attaching package: ‘gplots’

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

lowess

Loading required package: ggplot2
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
line 1 did not have 13 elements
Calls: read.table -> scan
Execution halted
ALL done

Hi Weiming,

I am trying to run PCA analysis to a VCF with 2,659 samples and 17,110,876 variants. However, I got this error after running with default parameters. Could you help check with it? Thanks for your time!

Leo

Running log:
#warning skip Indel site, there are total skip Indel sites number is : 3252724
#Warning skip non bi-allelic(Singleton/ThreeMulti allelic) site, and total skip allelic sites number is :284
#Warning skip high missing site, and total skip allelic sites number is :1040298
#Warning skip low Minor Allele Frequency site, and total skip allelic sites number is :370246
#Warning skip Sex chr Site, and total skip allelic sites number is :632171
#After Filtering, total Number of 11815153 SNPs were taken for the PCA calculation
Start To Create Normalized_IBS/Yang/BaldingNicolsKinship ...
Eigenvalues of 2659 individuals have been saved in [ PCAanalysis.eigenval ].
EM init K by auto of K-mean, Best cluster K = 1
VCF2PCACluster: ./include/Eigen/src/Core/DenseCoeffsBase.h:427: Eigen::DenseCoeffsBase<Derived, 1>::Scalar& Eigen::DenseCoeffsBase<Derived, 1>::operator()(Eigen::Index) [with Derived = Eigen::Matrix<int, -1, 1>; Eigen::DenseCoeffsBase<Derived, 1>::Scalar = int; Eigen::Index = long int]: Assertion `index >= 0 && index < size()' failed.
/var/spool/pbs/mom_priv/jobs/1410896.omics.SC: line 11: 164918 Aborted (core dumped) VCF2PCACluster -InVCF Merged.hg38.GnomADcommonVariants.norm.rmDup.rmNonAlt.vcf.gz -OutPut PCAanalysis

请问作者大大 eigenval 文件是否代表每个 PC 的解释比例，如果是的话，是不是我的样本 PC1/2/3 都有些太小了！谢谢！

RT