<p>将vcf格式转化为maf格式&#xff0c;跑的命令是&#xff1a;</p> 

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全部报错内容：（其实最根本的就是题目那句error）

——————– EXCEPTION ——————– MSG: ERROR: Cache directory /home/.vep/homo_sapiens_refseq/88_GRCh38/homo_sapiens not found STACK Bio::EnsEMBL::VEP::CacheDir::dir /home/software/miniconda3/envs/GC/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:182 STACK Bio::EnsEMBL::VEP::CacheDir::init /home/software/miniconda3/envs/GC/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:139 STACK Bio::EnsEMBL::VEP::CacheDir::new /home/software/miniconda3/envs/GC/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:68 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /home/software/miniconda3/envs/GC/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:75 STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /home/software/miniconda3/envs/GC/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:63 STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /home/software/miniconda3/envs/GC/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:123 STACK Bio::EnsEMBL::VEP::Runner::init /home/software/miniconda3/envs/GC/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/Runner.pm:77 STACK Bio::EnsEMBL::VEP::Runner::run /home/software/miniconda3/envs/GC/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/Runner.pm:111 STACK toplevel /home/software/miniconda3/envs/GC/bin//vep:209 Date (localtime) = Mon Oct 28 15:35:01 2024 Ensembl API version = 88 ————————————————— ERROR: Failed to run the VEP annotator! Command: /home/software/miniconda3/envs/GC/bin/perl ‘/home/software/miniconda3/envs/GC/bin//vep’ –species homo_sapiens –assembly GRCh38 –no_progress –no_stats –buffer_size 5000 –sift b –ccds –uniprot –hgvs –symbol –numbers –domains –gene_phenotype –canonical –protein –biotype –uniprot –tsl –variant_class –shift_hgvs 1 –check_existing –total_length –allele_number –no_escape –xref_refseq –failed 1 –vcf –flag_pick_allele –pick_order canonical,tsl,biotype,rank,ccds,length –dir ‘/home/.vep/homo_sapiens_refseq/88_GRCh38’ –fasta ‘https://blog.csdn.net/_/article/Homo_sapiens.GRCh38.dna.toplevel.fa' –format vcf –input_file ’sample1.vcf‘ –output_file ’https://blog.csdn.net/_/article/details/sample1.vep.vcf' –offline –pubmed –fork 4 –polyphen b –af –af_1kg –regulatory

 根本问题：VEP 在/home/.vep/homo_sapiens_refseq/88_GRCh38/homo_sapiens路径下找不到缓存文件目录。

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解决方法：

由于根本问题是找不到缓存，我们先下载缓存。由于我的参考基因是GRCh38，因此下载对应的vep缓存，手动自动都行，要是自动下载太慢就手动：

手动下载：https://ftp.ensembl.org/pub/release-88/variation/VEP/homo_sapiens_vep_88_GRCh38.tar.gz

自动下载：

下载后解压。下载的文件就是homo_sapiens，注意解压后位置，放到对应代码报错找不到的位置里，即/home/.vep/homo_sapiens_refseq/88_GRCh38目录下。VEP 的缓存应该是包含一个特定的文件，包括物种名称和基因组版本等内容。查看最终的路径，存在：/home/.vep/homo_sapiens_refseq/88_GRCh38/homo_sapiens/88_GRCh38

再跑一遍命令代码，就可以成功运行啦！