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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.
The text was updated successfully, but these errors were encountered:
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:
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.
The text was updated successfully, but these errors were encountered: