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mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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ERROR: Failed to run the VEP annotator! #342

Open SuiyueWestlake opened 1 year ago

SuiyueWestlake commented 1 year ago

I installed VEP through conda install -c bioconda ensembl-vep .

And my command for vcf2maf is perl vcf2maf.pl --input-vcf 915.raw.somatic.vcf --output-maf 915.raw.somatic.maf --ref-fasta /storage/publicdata/ref/bwa/hg38_GATK/genome.fa --remap-chain /storage/lixuLab/suiyue/CHEK1/WES/clean_data/gatk/Separate/annovar/mskcc-vcf2maf-754d68a/data/hg38_to_GRCh38.chain --vep-path /home/lixuLab/suiyue/miniconda3/envs/WES/share/ensembl-vep-88.9-0

But I got the error. ERROR: Failed to run the VEP annotator!

I would appreciate it if anyone could help.

Joyjoyjoyc commented 2 weeks ago

Hi, @SuiyueWestlake! I got a similar problem with you, I got the error message below STATUS: Running VEP and writing to: WCD160319_rna/gatk/WCD160319_rna_withpon_norm.vep.vcf 2024-10-31 09:48:48 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this substr outside of string at /home/cuiyiran/miniconda3/envs/vep/share/ensembl-vep-112.0-0/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 914, <__ANONIO__> line 583050. Died in forked process 9730

ERROR: Failed to run the VEP annotator! I wonder if you had already figure it out? Thank you!