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Ensembl / ensembl-vep

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
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Annotation on small file not finished after 1 day #1330

Open adrian-keda opened 1 year ago

adrian-keda commented 1 year ago

I need to annotate some indels for chromosome 22, and then scale this step to the full human genome. I'm running vep locally using snakemake in a HPC environment with 75Gb of RAM. The input file has ~30k variants and it's size is 21Mb. My jobs are 24 hour limited and vep doesn't finish annotating. While the job was running, I periodically checked the file being written and it never updated, it only showed the vcf header.

System

Full VEP command line

vep -i input.vcf \ --format vcf \ --fork 10 \ --offline \ --cache \ --dir_cache resources/cache2 \ --cache_version 108 \ --species homo_sapiens \ --assembly GRCh37 \ --force_overwrite \ --phased \ --transcript_filter 'stable_id' \ --dir_plugins resources/VEP_plugins \ --plugin SpliceAI,snv=resources/plugins_scores/spliceai/scores/spliceai_scores.raw.snv.hg19.vcf.gz,indel=resources/plugins_scores/spliceai/scores/spliceai_scores.raw.indel.hg19.vcf.gz \ --plugin LoFtool,resources/plugins_scores/loftool/scores/LoFtool_scores.txt \ --symbol \ --canonical \ --tab \ --fields 'Uploaded_variation,Location,Allele,Gene,SYMBOL,Feature,Feature_type,Consequence,cDNA_position,Protein_position,Amino_acids,Codons,IMPACT,DISTANCE,EXON,FLAGS,BIOTYPE,CANONICAL,LoFtool,SpliceAI_pred' \ --fasta resources/homo_sapiens_fasta/108_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa \ -o output.vcf

Full error message

No warnings or errors raised.

Data files

likhitha-surapaneni commented 1 year ago

Hi @adrian-keda , thank you for providing us the details.

Can you please try the following and let us know the results. This will help us in understanding the issue better:

  1. Running the same command with a small set of variants
  2. Running with the original input but without the SpiceAI plugin
adrian-keda commented 1 year ago

Hi!

We haven't tried the first solution yet. The other one seems to be working properly, the job finishes quite fast. But, I need to run it using SpliceAI because I need those scores for my current task.

Could it be a bug or is there any I can include those scores during the annotation process?

Thanks for your help!

likhitha-surapaneni commented 1 year ago

Hi @adrian-keda ,

Thank you for trying out the above commands. We are looking into the issue from our end and will let you know once we have an update.

Kind regards, Likhitha