WARNING: Failed to compile plugin LoF: can't open!

scha36 commented 5 years ago

Hi, I'm struggling to set LoF plugin in my VEP. After installing LoF.pm and related files addressed in here, I ran vep using script below:

vep98=/data/software/VEP/ensembl-vep-release-98 perl $vep98/vep \ --cache --dir_cache $vep98/cache \ -i $1.vcf -o $1.vep.vcf \ --assembly GRCh38 --symbol --vcf --exclude_predicted \ --fasta $vep98/cache/homo_sapiens/98_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa \ --minimal --allele_number 50 --no_stats \ --pick --force_overwrite --offline --fork 20 \ --plugin LoF,loftee_path:$vep98/Plugins/loftee,human_ancestor_fa:$vep98/Plugins/loftee/human_ancestor.fa.gz \ --dir_plugins /data/software/VEP/ensembl-vep-release-98/Plugins

Unfortunately, I got some errors and I have no idea how I can figure out this issue.

WARNING: Failed to compile plugin LoF: can't open! Compilation failed in require at /data/software/VEP/ensembl-vep-release-98/Plugins/loftee/loftee_splice_utils.pl line 4. Compilation failed in require at /data/software/VEP/ensembl-vep-release-98/Plugins/LoF.pm line 33. Compilation failed in require at (eval 219) line 2. BEGIN failed--compilation aborted at (eval 219) line 2.

Any suggestion? Thanks in advance!

emauryg commented 4 years ago

I have the same issue, has it been resolved?

hcurley commented 4 years ago

I fixed the issue by writing the full paths to my files on respective lines: loftee_splice_utils.pl > line 4, line 5, line 212 LoF.pm > line 83

This then worked for me.

konradjk / loftee

WARNING: Failed to compile plugin LoF: can't open! #60