(base) 08:04 jhz22@login-e-10 ~/rds/public_databases/ensembl-vep $ perl INSTALL.pl -l Bio -y GRCh38 -a acfp -g all -s homo_sapiens_merged --NO_TEST -c .vep

Setting up directories
 - fetching BioPerl
 - unpacking ./Bio/tmp/release-1-6-924.zip
 - moving files

Downloading required Ensembl API files
 - fetching ensembl
 - unpacking ./Bio/tmp/ensembl.zip
 - moving files
 - getting version information
 - fetching ensembl-variation
 - unpacking ./Bio/tmp/ensembl-variation.zip
 - moving files
 - getting version information
 - fetching ensembl-funcgen
 - unpacking ./Bio/tmp/ensembl-funcgen.zip
 - moving files
 - getting version information
 - fetching ensembl-io
 - unpacking ./Bio/tmp/ensembl-io.zip
 - moving files
 - getting version information
 - getting list of available cache files
 - downloading ftp://ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_vep_104_GRCh38.tar.gz
 - unpacking homo_sapiens_vep_104_GRCh38.tar.gz
 - converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster
 - use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later)
2021-10-14 23:06:50 - Processing homo_sapiens
2021-10-14 23:06:50 - Processing version 104_GRCh38
2021-10-14 23:06:51 - No unprocessed types remaining, skipping
2021-10-14 23:06:51 - All done!
 - downloading Homo_sapiens.GRCh38.dna.toplevel.fa.gz
 - extracting data
 - attempting to index
 - indexing FASTA file
 - indexing OK

The FASTA file should be automatically detected by the VEP when using --cache or --offline.
If it is not, use "--fasta .vep/homo_sapiens/104_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa"

NB: Remember to use --merged when running the VEP with this cache!
 - downloading ftp://ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_merged_vep_104_GRCh38.tar.gz
 - unpacking homo_sapiens_merged_vep_104_GRCh38.tar.gz
 - converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster
 - use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later)
2021-10-15 08:56:03 - Processing homo_sapiens_merged
2021-10-15 08:56:03 - Processing version 104_GRCh38
2021-10-15 08:56:03 - INFO: BAM-edited cache detected, enabling --use_transcript_ref; use --use_given_ref to override this
2021-10-15 08:56:03 - No unprocessed types remaining, skipping
2021-10-15 08:56:03 - All done!
 - downloading Homo_sapiens.GRCh38.dna.toplevel.fa.gz
 - extracting data
 - attempting to index
 - indexing FASTA file
 - indexing OK

The FASTA file should be automatically detected by the VEP when using --cache or --offline.
If it is not, use "--fasta .vep/homo_sapiens_merged/104_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa"

WARNING: The following plugins have not been found: all
Available plugins: AncestralAllele,Blosum62,CADD,CSN,Carol,Condel,Conservation,DisGeNET,Downstream,Draw,ExAC,ExACpLI,FATHMM,FATHMM_MKL,FlagLRG,FunMotifs,G2P,GO,GeneSplicer,Gwava,HGVSIntronOffset,LD,LOVD,LoF,LoFtool,LocalID,MPC,MTR,Mastermind,MaxEntScan,NearestExonJB,NearestGene,PON_P2,Phenotypes,PostGAP,ProteinSeqs,REVEL,ReferenceQuality,SameCodon,SingleLetterAA,SpliceAI,SpliceRegion,StructuralVariantOverlap,SubsetVCF,TSSDistance,dbNSFP,dbscSNV,gnomADc,miRNA,neXtProt,satMutMPRA

 - installing "AncestralAllele"
 - This plugin requires data
 - See .vep/Plugins/AncestralAllele.pm for details
 - OK

 - installing "Blosum62"
 - add "--plugin Blosum62" to your VEP command to use this plugin
 - OK

 - installing "CADD"
 - This plugin requires data
 - See .vep/Plugins/CADD.pm for details
 - OK

 - installing "CSN"
 - add "--plugin CSN" to your VEP command to use this plugin
 - OK

 - installing "Carol"
 - This plugin requires installation
 - See .vep/Plugins/Carol.pm for details
 - OK

 - installing "Condel"
 - This plugin requires installation
 - See .vep/Plugins/Condel.pm for details
 - OK

 - installing "Conservation"
 - add "--plugin Conservation,[options]" to your VEP command to use this plugin
 - OK

 - installing "DisGeNET"
 - add "--plugin DisGeNET" to your VEP command to use this plugin
 - OK

 - installing "Downstream"
 - add "--plugin Downstream" to your VEP command to use this plugin
 - OK

 - installing "Draw"
 - This plugin requires installation
 - See .vep/Plugins/Draw.pm for details
 - OK

 - installing "ExAC"
 - This plugin requires data
 - See .vep/Plugins/ExAC.pm for details
 - OK

 - installing "ExACpLI"
 - This plugin requires data
 - See .vep/Plugins/ExACpLI.pm for details
 - OK

 - installing "FATHMM"
 - add "--plugin FATHMM" to your VEP command to use this plugin
 - OK

 - installing "FATHMM_MKL"
 - This plugin requires data
 - See .vep/Plugins/FATHMM_MKL.pm for details
 - OK

 - installing "FlagLRG"
 - add "--plugin FlagLRG" to your VEP command to use this plugin
 - OK

 - installing "FunMotifs"
 - add "--plugin FunMotifs" to your VEP command to use this plugin
 - OK

 - installing "G2P"
 - This plugin requires data
 - See .vep/Plugins/G2P.pm for details
 - OK

 - installing "GO"
 - add "--plugin GO" to your VEP command to use this plugin
 - OK

 - installing "GeneSplicer"
 - This plugin requires installation
 - See .vep/Plugins/GeneSplicer.pm for details
 - OK

 - installing "Gwava"
 - This plugin requires data
 - See .vep/Plugins/Gwava.pm for details
 - OK

 - installing "HGVSIntronOffset"
 - add "--plugin HGVSIntronOffset" to your VEP command to use this plugin
 - OK

 - installing "LD"
 - add "--plugin LD,[options]" to your VEP command to use this plugin
 - OK

 - installing "LOVD"
 - add "--plugin LOVD" to your VEP command to use this plugin
 - OK

 - installing "LoF"
 - This plugin requires installation
 - This plugin requires data
 - See .vep/Plugins/LoF.pm for details
 - OK

 - installing "LoFtool"
 - This plugin requires data
 - See .vep/Plugins/LoFtool.pm for details
 - OK

 - installing "LocalID"
 - add "--plugin LocalID" to your VEP command to use this plugin
 - OK

 - installing "MPC"
 - This plugin requires data
 - See .vep/Plugins/MPC.pm for details
 - OK

 - installing "MTR"
 - This plugin requires data
 - See .vep/Plugins/MTR.pm for details
 - OK

 - installing "Mastermind"
 - add "--plugin Mastermind" to your VEP command to use this plugin
 - OK

 - installing "MaxEntScan"
 - This plugin requires installation
 - See .vep/Plugins/MaxEntScan.pm for details
 - OK

 - installing "NearestExonJB"
 - add "--plugin NearestExonJB" to your VEP command to use this plugin
 - OK

 - installing "NearestGene"
 - add "--plugin NearestGene" to your VEP command to use this plugin
 - OK

 - installing "PON_P2"
 - add "--plugin PON_P2" to your VEP command to use this plugin
 - OK

 - installing "Phenotypes"
 - This plugin requires data
 - See .vep/Plugins/Phenotypes.pm for details
 - OK

 - installing "PostGAP"
 - add "--plugin PostGAP" to your VEP command to use this plugin
 - OK

 - installing "ProteinSeqs"
 - add "--plugin ProteinSeqs" to your VEP command to use this plugin
 - OK

 - installing "REVEL"
 - This plugin requires data
 - See .vep/Plugins/REVEL.pm for details
 - OK

 - installing "ReferenceQuality"
 - add "--plugin ReferenceQuality" to your VEP command to use this plugin
 - OK

 - installing "SameCodon"
 - add "--plugin SameCodon" to your VEP command to use this plugin
 - OK

 - installing "SingleLetterAA"
 - add "--plugin SingleLetterAA" to your VEP command to use this plugin
 - OK

 - installing "SpliceAI"
 - add "--plugin SpliceAI" to your VEP command to use this plugin
 - OK

 - installing "SpliceRegion"
 - add "--plugin SpliceRegion" to your VEP command to use this plugin
 - OK

 - installing "StructuralVariantOverlap"
 - add "--plugin StructuralVariantOverlap" to your VEP command to use this plugin
 - OK

 - installing "SubsetVCF"
 - add "--plugin SubsetVCF" to your VEP command to use this plugin
 - OK

 - installing "TSSDistance"
 - add "--plugin TSSDistance" to your VEP command to use this plugin
 - OK

 - installing "dbNSFP"
 - This plugin requires installation
 - This plugin requires data
 - See .vep/Plugins/dbNSFP.pm for details
 - OK

 - installing "dbscSNV"
 - This plugin requires installation
 - This plugin requires data
 - See .vep/Plugins/dbscSNV.pm for details
 - OK

 - installing "gnomADc"
 - add "--plugin gnomADc" to your VEP command to use this plugin
 - OK

 - installing "miRNA"
 - add "--plugin miRNA" to your VEP command to use this plugin
 - OK

 - installing "neXtProt"
 - add "--plugin neXtProt" to your VEP command to use this plugin
 - OK

 - installing "satMutMPRA"
 - add "--plugin satMutMPRA" to your VEP command to use this plugin
 - OK

NB: One or more plugins that you have installed will not work without installation or downloading data; see logs above

All done