在callsnp过程中形成db文件时出错，但是可以形成db文件夹，我继续往下做，gvcf转化成vcf得到的结果文件没有SNP行，只有上边的注释行和表头

15:54:41.391 WARN GenomicsDBImport - GenomicsDBImport cannot use multiple VCF reader threads for initialization when the number of intervals is greater than 1. Falling back to serial VCF reader initialization.

15:54:41.529 WARN IntelInflater - Zero Bytes Written : 0

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15:54:41.617 INFO GenomicsDBImport - Importing batch 1 with 5 samples

15:54:41.618 INFO GenomicsDBImport - Importing batch 1 with 5 samples

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分类：GWAS

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马杰宇 2024-02-19 16:40

以下是我的命令：/public/software/singularity/bin/singularity exec /public/home/perl5/gwas-sif/reseq.sif \

bash -c "gatk --java-options "-Xmx20g" GenomicsDBImport \

-L chr.list --tmp-dir $tmpdir -R $REF --batch-size 5 \

--reader-threads 5 --max-num-intervals-to-import-in-parallel 5 \

--genomicsdb-workspace-path db --sample-name-map cohort.sample_map"

在callsnp过程中形成db文件时出错，但是可以形成db文件夹，我继续往下做，gvcf转化成vcf得到的结果文件没有SNP行，只有上边的注释行和表头

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