WARNING: Plugin 'LoF' went wrong: Can't locate object method "prepare" via package "false" (perhaps you forgot to load "false"?)

[xx3411]

Hello! I'm running vep from the https://github.com/konradjk/loftee/tree/master branch,

${DIR}/vep -i /dt19/share/BC0001/Level3/20210715/vcf/S002_DNM_V4_7_filtered_noAS.1.3.2.siteonly.dn.vcf.gz \ -o temp.vcf \ --vcf --dir_cache ${DIR}/vep_database --cache --species homo_sapiens --assembly GRCh37 \ --fasta ${DIR}/vep_database/Homo_sapiens.GRCh37.dna.primary_assembly.fa \ --force_overwrite \ --offline \ --plugin LoF,loftee_path:${DIR}/Plugins/loftee,human_ancestor_fa:${DIR}/Plugins/loftee/human_ancestor.fa.gz,phylocsf_data:${DIR}/Plugins/loftee/phylocsf_gerp.sql \ --dir_plugins ${DIR}/Plugins/loftee

and I'm getting a lot of warnings like this one

WARNING: Plugin 'LoF' went wrong: Can't locate object method "prepare" via package "false" (perhaps you forgot to load "false"?) at /public/home/xx2019/software/ensembl-vep/Plugins/loftee/gerp_dist.pl line 129.

How can I solve this problem?

[Jordi-Valls]

Hello I had the same problem as you, to solve it you have to download the sqlite "phylocsf_gerp.sql", you can downloaded from the link that readme provides in this github "The required SQL database (gzip) can be downloaded here."

Then you have to uncompress and finally, the argument that you have to include is conservation_file:/your/path/phylocsf_gerp.sql. Concretely near to human_ancestor_fa:${DIR}/Plugins/loftee/human_ancestor.fa.gz, something like this:

human_ancestor_fa:${DIR}/Plugins/loftee/human_ancestor.fa.gz,conservation_file:/your/path/phylocsf_gerp.sql

Using this argument with this file, the error disappears in my case.

Best,

Jordi

[jon4thin]

Hello I had the same problem as you, to solve it you have to download the sqlite "phylocsf_gerp.sql", you can downloaded from the link that readme provides in this github "The required SQL database (gzip) can be downloaded here."

Then you have to uncompress and finally, the argument that you have to include is conservation_file:/your/path/phylocsf_gerp.sql. Concretely near to human_ancestor_fa:${DIR}/Plugins/loftee/human_ancestor.fa.gz, something like this:

human_ancestor_fa:${DIR}/Plugins/loftee/human_ancestor.fa.gz,conservation_file:/your/path/phylocsf_gerp.sql

Using this argument with this file, the error disappears in my case.

Best,

Jordi

Thanks, this helped me get up and running

[xx3411]

thanks,it works. unfortunately, i am getting some warnings about LoF,WARNING: Plugin 'LoF' went wrong: -------------------- EXCEPTION -------------------- MSG: Slice start cannot be greater than slice end STACK Bio::EnsEMBL::Slice::expand /public/home/xx2019/software/ensembl-vep/Bio/EnsEMBL/Slice.pm:1217 STACK LoF::get_upstream_acceptor_flank /public/home/xx2019/software/ensembl-vep/Plugins/loftee/extended_splice.pl:209 STACK LoF::get_effect_on_splice /public/home/xx2019/software/ensembl-vep/Plugins/loftee/extended_splice.pl:111 STACK LoF::run /public/home/xx2019/software/ensembl-vep/Plugins/loftee/LoF.pm:188 STACK (eval) /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm:2072 STACK Bio::EnsEMBL::VEP::OutputFactory::run_plugins /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/OutputFactory.pm STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_VariationFeatureOverlapAllele_output_hashes /public/home/xx2019/software/ensembl-vep/ STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_output_hashes_by_VariationFeature /public/home/xx2019/software/ensembl-vep/modules/Bi STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_output_hashes_by_InputBuffer /public/home/xx2019/software/ensembl-vep/modules/Bio/Ens STACK Bio::EnsEMBL::VEP::OutputFactory::get_all_lines_by_InputBuffer /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP STACK Bio::EnsEMBL::VEP::Runner::_buffer_to_output /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:421 STACK Bio::EnsEMBL::VEP::Runner::next_output_line /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:369 STACK Bio::EnsEMBL::VEP::Runner::run /public/home/xx2019/software/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:207 STACK toplevel /public/home/xx2019/software/ensembl-vep/vep:240 Date (localtime) = Sat Aug 19 05:29:12 2023 Ensembl API version = 108