似乎是 vcf2pca 在使用 Eigen 库处理矩阵时出现了断言失败，可能是是矩阵索引超出了有效范围。

[chanity256]

vcf2pca: src/./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/slurm/d/job16383335/slurm_script: line 8: 24083 Aborted (core dumped) vcf2pca -InVCF /public/agis/changyuxiao_group/wanghaonan/project/02_pepper/07_snp.vcf/merged_496pepper.snp.filtered.miss0.2maf0.05.vcf.recode.vcf -OutPut vcf2pca.pepper.miss0.2maf0.05

这是日志的输出内容。

这是我的代码：

1.合并所有的gvcf并进行joint callling

查找所有的 GVCF 文件

#gvcf_files=$(find $gvcfgz_dir -type f -name "*.gvcf.gz")

构建输入文件列表并执行 Sentieon 命令

#$SENTIEON_INSTALL_DIR/bin/sentieon driver -t $nt -r $reference
#--algo GVCFtyper
#$(for file in $gvcf_files; do echo -n "-v $file "; done)
#$output_vcf/${name_merged}.vcf

2.对合并的vcf文件SelectVariants-提取 SNPs

#gatk --java-options "-Xmx50g" SelectVariants -R $reference -select-type-to-include SNP -V $output_vcf/${name_merged}.vcf -O $output_vcf/${name_merged}.snp.vcf

3.VariantFiltration SNP 硬过滤，并去除低质量的 SNP（也就是有SNP_Filter标记的行）

#gatk --java-options "-Xmx50g" VariantFiltration -V $output_vcf/${name_merged}.snp.vcf --filter-expression 'QD < 2.0 || MQ < 40.0 || FS > 60.0 || SOR > 3.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0' --filter-name 'SNP_Filter' -O $output_vcf/${name_merged}.snp.filtering.vcf

#less $output_vcf/${name_merged}.snp.filtering.vcf | grep -v "SNP_Filter" > $output_vcf/${name_merged}.snp.filtered.vcf

4.vcftools再过滤

vcftools --vcf $output_vcf/${name_merged}.snp.filtered.vcf --max-missing 0.2 --maf 0.05 --recode --recode-INFO-all --out $output_vcf/${name_merged}.snp.filtered.REmiss0.2maf0.05.vcf