Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

ERROR: No cache found for homo_sapiens, version 93 #360

Open
Olsennnnn opened this issue Sep 12, 2024 · 0 comments
Open

ERROR: No cache found for homo_sapiens, version 93 #360

Olsennnnn opened this issue Sep 12, 2024 · 0 comments

Comments

@Olsennnnn
Copy link

Hi,
I want to convert the vcf file to the maf file, but an error occurs when I run the following code:perl vcf2maf.pl --input-vcf 10084_10084.vcf --output-maf 10084_10084.maf --vep-path /home/data/t230420/miniconda3/envs/vep/bin --vep-data /home/data/t230420 --ref-fasta /home/data/t230420/hg18.fa --vep-forks 1 --tumor-id 10084_10084 --filter-vcf 0.
The error is:

WARNING: Couldn't retrieve bps around 23:152850324 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 23:152880620 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 23:152892914 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 23:152901148 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 23:153313264 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 25:214201 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 25:1946325 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 25:1948777 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 25:154685032 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 25:154745988 from reference FASTA: /home/data/t230420/hg18.fa
WARNING: Couldn't retrieve bps around 26:5443 from reference FASTA: /home/data/t230420/hg18.fa
STATUS: Running VEP and writing to: ./10084_10084.vep.vcf
Possible precedence issue with control flow operator at /home/data/t230420/miniconda3/envs/vep/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 845.

-------------------- EXCEPTION --------------------
MSG: ERROR: No cache found for homo_sapiens, version 93

STACK Bio::EnsEMBL::VEP::CacheDir::dir /home/data/t230420/miniconda3/envs/vep/share/ensembl-vep-93.2-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:328
STACK Bio::EnsEMBL::VEP::CacheDir::init /home/data/t230420/miniconda3/envs/vep/share/ensembl-vep-93.2-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:227
STACK Bio::EnsEMBL::VEP::CacheDir::new /home/data/t230420/miniconda3/envs/vep/share/ensembl-vep-93.2-0/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all_from_cache /home/data/t230420/miniconda3/envs/vep/share/ensembl-vep-93.2-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:115
STACK Bio::EnsEMBL::VEP::AnnotationSourceAdaptor::get_all /home/data/t230420/miniconda3/envs/vep/share/ensembl-vep-93.2-0/modules/Bio/EnsEMBL/VEP/AnnotationSourceAdaptor.pm:91
STACK Bio::EnsEMBL::VEP::BaseRunner::get_all_AnnotationSources /home/data/t230420/miniconda3/envs/vep/share/ensembl-vep-93.2-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:175
STACK Bio::EnsEMBL::VEP::Runner::init /home/data/t230420/miniconda3/envs/vep/share/ensembl-vep-93.2-0/modules/Bio/EnsEMBL/VEP/Runner.pm:123
STACK Bio::EnsEMBL::VEP::Runner::run /home/data/t230420/miniconda3/envs/vep/share/ensembl-vep-93.2-0/modules/Bio/EnsEMBL/VEP/Runner.pm:194
STACK toplevel /home/data/t230420/miniconda3/envs/vep/bin/vep:224
Date (localtime)    = Thu Sep 12 09:31:55 2024
Ensembl API version = 93
---------------------------------------------------

ERROR: Failed to run the VEP annotator! Command: /home/data/t230420/miniconda3/envs/vep/bin/perl /home/data/t230420/miniconda3/envs/vep/bin/vep --species homo_sapiens --assembly GRCh37 --offline --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --pubmed --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/data/t230420 --fasta /home/data/t230420/hg18.fa --format vcf --input_file 10084_10084.vcf --output_file ./10084_10084.vep.vcf --polyphen b --af --af_1kg --af_esp --af_gnomad --regulatory

It's been determined that the human reference genome I'm going to use is hg18.
The vep version used in the current environment is 93.2.
What can I do to solve this problem?

Thank you.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant