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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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the web file has no image #1663

Open fan040 opened 2 months ago

fan040 commented 2 months ago

Describe the issue

There is no picture in the vep web file I generated. I would like to ask if I have that plug-in not installed? image

Full VEP command line

apprainer run vep.sif vep --format vcf -i merge.snp_idl.2allele.resume.vcf --vcf -o output/merge.snp_idl.2allele.resume.out.vcf --species triticum_aestivum --force_overwrite --plugin NMD --gff /cluster/home/fanrong/database/AK58/fasta/AK58v4MP.gff3.gz --fasta /cluster/home/fanrong/database/AK58/fasta/wheat_AK58v4MP.genome.fa

likhitha-surapaneni commented 2 months ago

Hi @fan040, sorry to hear that you are facing issues. Can you please provide us with the input file, gff and fasta files used?

Thank you

fan040 commented 2 months ago

I am very sorry that my file is too large, it is very difficult to upload, and the file is confidential. I can take some pictures, is that OK? Besides, my text file seems to be output normally? image

likhitha-surapaneni commented 2 months ago

Hi @fan040 ,

Thank you for the picture, is there any warning file generated or are there any warnings in the standard output when the command was run?

fan040 commented 2 months ago

Thank you for your reply. There are indeed some errors in the operation of my program. Is this the cause? image

likhitha-surapaneni commented 2 months ago

Hi @fan040, Thank you for the details.

Is it possible to run an example variant with --database or --cache options to see if the plugin is installed correctly?

Please also let us know if a smaller version of the input and gff files can be shared in order to reproduce the issue.