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I installed the latest version of VEP from Github and ensembleVEP from Bioconductor with version 105 of the annotation cache on ubuntu 18.04. When I am running the steps from the ensemblVEP R tutorial, I get the following errors. Please help me!

library(ensemblVEP)
param <- VEPFlags()
Error in validObject(.Object) :
invalid class “VEPFlags” object: Ensembl >=88 requires vep script (not variant_effect_predictor.pl)

Hi Lori,

Submitting a github issue for something we already talked about on the support site (here: https://support.bioconductor.org/p/106976/#107036).

I ran into trouble using v88 of the VEP script with ensemblVEP, because the default host used by the bioc module (useastdb.ensembl.org) does not support anything other than the current or current minus 1 versions of the vep script (according to https://www.ensembl.org/info/data/mysql.html), and the script gives a very uninformative error if you try to use an older version of the vep script with the US host, whether on command line or through R/Bioc.

Here's the example code - this fails for me with a mysterious error:

library(ensemblVEP)
file <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")

myparam88a <- VEPParam( version=88, dataformat=c(vcf=TRUE)) 
vcf88a <- ensemblVEP(file, param=myparam88a)
#Can't use an undefined value as an ARRAY reference at #/home/jayoung/malik_lab_shared/perl/ensembl/modules/Bio/EnsEMBL/Registry.pm line 2546.
#Error in .io_check_exists(path(con)) : file(s) do not exist:
#  '/tmp/Rtmpi8eJw2/file52c81bd6649'

when I specify a different host it works fine:

myparam88b <- VEPParam( version=88, dataformat=c(vcf=TRUE), database=c(host="ensembldb.ensembl.org")) 
vcf88b <- ensemblVEP(file, param=myparam88b)
 

Would it be possible to change the default host when older versions of VEP are specified? I didn't expect that to be an issue, because on my real data I was using a local cached database and didn't think I was contacting any host at all. The same fix works on my data, though, so I'm happy:

tempVEPcacheDir <- "/fh/fast/malik_h/grp/public_databases/Ensembl/VariantEffectPredictorCache"
tempVEPpluginsDir <- "/fh/fast/malik_h/grp/public_databases/Ensembl/VariantEffectPredictorCache/plugins"

## this fails: 
myparamsYeast88a <- VEPParam( version=88,
                            input=c(species="saccharomyces_cerevisiae"), 
                            cache=c(cache=TRUE, dir=tempVEPcacheDir,
                                dir_cache=tempVEPcacheDir, dir_plugins=tempVEPpluginsDir),
                            database=c(database=FALSE),
                            dataformat=c(vcf=TRUE) ) 
tempTest88a <- ensemblVEP(testFile, myparamsYeast88a) 
#Can't use an undefined value as an ARRAY reference at #/home/jayoung/malik_lab_shared/perl/ensembl/modules/Bio/EnsEMBL/Registry.pm line 2546.
#Error in .io_check_exists(path(con)) : file(s) do not exist:
#  '/tmp/RtmpxuFFsr/file560c5748392c'

## this works:
myparamsYeast88b <- VEPParam( version=88,
                            input=c(species="saccharomyces_cerevisiae"), 
                            cache=c(cache=TRUE, dir=tempVEPcacheDir,
                                dir_cache=tempVEPcacheDir, dir_plugins=tempVEPpluginsDir),
                            database=c(database=FALSE, host="ensembldb.ensembl.org"),
                            dataformat=c(vcf=TRUE) ) 
tempTest88b <- ensemblVEP(testFile, myparamsYeast88b) 
 

Session info is below (truncated). Thanks,

Janet

sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

other attached packages:
[1] ensemblVEP_1.20.1          VariantAnnotation_1.22.3
[3] Rsamtools_1.28.0           Biostrings_2.44.2         
[5] XVector_0.16.0             SummarizedExperiment_1.6.0
[7] DelayedArray_0.2.0         matrixStats_0.52.2        
[9] Biobase_2.36.0             GenomicRanges_1.28.4      
[11] GenomeInfoDb_1.12.0        IRanges_2.10.3            
[13] S4Vectors_0.14.0           BiocGenerics_0.22.0    

I installed the latest version of VEP from Github and ensembleVEP from Bioconductor with version 95 of the annotation cache on Centos OS. When I am running the steps from the ensemblVEP R tutorial, I get the following errors. Please advise.

library(ensemblVEP)
param <- VEPFlags()
Error in validObject(.Object) :
invalid class “VEPFlags” object: Ensembl >=88 requires vep script (not variant_effect_predictor.pl)
param <- VEPFlags(flags=list(host="useastdb.ensembl.org"), version=94)
Error in validObject(.Object) :
invalid class “VEPFlags” object: Ensembl >=88 requires vep script (not variant_effect_predictor.pl)

I have installed vep and am trying to run it from the ensembl-vep bioconductor package. When loading the library, I am getting the following warning:

Warning message:
In system2("perl", .getVepPath(), stdout = TRUE, stderr = TRUE) :
running command ''perl' /usr/local/bin/vep 2>&1' had status 134

When I run the system command directly on the console, I get:

system("perl /usr/local/bin/vep 2>&1")
dyld: lazy symbol binding failed: Symbol not found: _Perl_xs_handshake
Referenced from: /Users/jthill/Code/ensembl-vep/Faidx.bundle
Expected in: flat namespace

dyld: Symbol not found: _Perl_xs_handshake
Referenced from: /Users/jthill/Code/ensembl-vep/Faidx.bundle
Expected in: flat namespace

sh: line 1: 8906 Abort trap: 6 perl /usr/local/bin/vep 2>&1

On the other hand, when I run the same command on the command line it works fine. I dug a little more, and I found that R is using the system perl ("usr/bin/perl") instead of the ensembl-recommended perlbrew installation. There needs to be a way for ensemblVEP to recognize perlbrew...

Hi there,

For troubleshooting purposes, it'd be great to add an option to the ensemblVEP function show the system call that's made to the vep script. See https://support.bioconductor.org/p/106976/

thanks,

Janet

I successfully installed VEP in my ubuntu v.20 and added its path to ~/.bashrc as shown below but still I get the error
.bashrc file content

export PATH="$PATH:/home/subudhak/ensembl-vep-release-108"
alias vep="sudo /home/subudhak/ensembl-vep-release-108/vep"

Error msg

Error in validObject(.Object) : 
  invalid class “VEPFlags” object: Ensembl >=88 requires vep script  (not variant_effect_predictor.pl)

When trying to explicitly define the path the error message persists: (even renamed vep to variant_effect_predictor.pl)

param <- VEPFlags(flags=list(host="useastdb.ensembl.org"), scriptPath = as.character("home/subudhak/ensembl-vep-release-108/variant_effect_predictor.pl"))
Error in validObject(.Object) : 
  invalid class “VEPFlags” object: Ensembl >=88 requires vep script  (not variant_effect_predictor.pl)