Hey! I am having the following issue when running VEP in singularity with loftee plugin
`bash-5.1$ singularity exec $HOME/vep.sif vep --dir $HOME/vep_data -i $HOME/ensembl/ensembl-vep/examples/homo_sapiens_GRCh38.vcf --refseq --regulatory --cache --cache_version 113 --plugin LoF,loftee_path:/users/diasfrazer/fbilleci/.vep/Plugins/loftee/
WARNING: Failed to compile plugin LoF: Can't locate utr_splice.pl in @inc (@inc contains: /plugins /opt/vep/src/ensembl-vep/modules /opt/vep/src/ensembl-vep /plugins /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) at /plugins/LoF.pm line 26.
Compilation failed in require at (eval 53) line 2.
BEGIN failed--compilation aborted at (eval 53) line 2.
2025-07-14 17:33:46 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this
2025-07-14 17:33:46 - INFO: Database will be accessed when using --use_transcript_ref
`
Thank you very much!
Federico
Hey! I am having the following issue when running VEP in singularity with loftee plugin
`bash-5.1$ singularity exec $HOME/vep.sif vep --dir $HOME/vep_data -i $HOME/ensembl/ensembl-vep/examples/homo_sapiens_GRCh38.vcf --refseq --regulatory --cache --cache_version 113 --plugin LoF,loftee_path:/users/diasfrazer/fbilleci/.vep/Plugins/loftee/
WARNING: Failed to compile plugin LoF: Can't locate utr_splice.pl in @inc (@inc contains: /plugins /opt/vep/src/ensembl-vep/modules /opt/vep/src/ensembl-vep /plugins /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.34.0 /usr/local/share/perl/5.34.0 /usr/lib/x86_64-linux-gnu/perl5/5.34 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl-base /usr/lib/x86_64-linux-gnu/perl/5.34 /usr/share/perl/5.34 /usr/local/lib/site_perl) at /plugins/LoF.pm line 26.
Compilation failed in require at (eval 53) line 2.
BEGIN failed--compilation aborted at (eval 53) line 2.
2025-07-14 17:33:46 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this
2025-07-14 17:33:46 - INFO: Database will be accessed when using --use_transcript_ref
`
Thank you very much!
Federico