Hi,
I would like to run ensemblVEP (without cache) with a list SNPs in a project that runs with human genome version 37.
On command line this works fine:
$ vep -i some.vcf --database --assembly GRCh37 --port 3337
'vep' instructs me to use '--port 3337':
"If using human GRCh37 add "--port 3337" to use the GRCh37 database, or --offline to avoid database connection entirely"
But in R:
> param <- VEPParam()
> input(param)$species <- "homo_sapiens"
> input(param)$assembly <- "GRCh37"
> database(param)$port <- 3337
> anno37 <- ensemblVEP( some_vcf_file ,param = param)
DBI connect('host=useastdb.ensembl.org;port=3337','anonymous',...) failed: Can't connect to MySQL server on 'useastdb.ensembl.org' (111) at //ensembl-vep/Bio/EnsEMBL/Registry.pm line 1767.
-------------------- EXCEPTION --------------------
MSG: Cannot connect to the Ensembl MySQL server at useastdb.ensembl.org:3337; check your settings & DBI error message: Can't connect to MySQL server on 'useastdb.ensembl.org' (111)
STACK Bio::EnsEMBL::Registry::load_registry_from_db /home/arvasmi/Work/Install/ensembl-vep/Bio/EnsEMBL/Registry.pm:1767
STACK Bio::EnsEMBL::VEP::BaseVEP::registry /home/arvasmi/Work/Install/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:163
STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /home/arvasmi/Work/Install/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:80
STACK Bio::EnsEMBL::VEP::Runner::init /home/arvasmi/Work/Install/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:72
STACK Bio::EnsEMBL::VEP::Runner::run /home/arvasmi/Work/Install/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:111
STACK toplevel /home/arvasmi/Work/Install/ensembl-vep//vep:209
Date (localtime) = Thu May 11 21:44:09 2017
Ensembl API version = 88
---------------------------------------------------
Error in .io_check_exists(path(con)) : file(s) do not exist:
'/tmp/RtmpaEiWiy/file5e6d53059560'
From the out set it seems that ensemblVEP is not passing the parameters properly to vep itself. Of course I can go around this, but in case I am not just doing something stupid in here, maybe it would be good to fix.
Best,
Mikko
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=fi_FI.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=fi_FI.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=fi_FI.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fi_FI.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] ensemblVEP_1.16.0 VariantAnnotation_1.22.0 Rsamtools_1.28.0 Biostrings_2.44.0 XVector_0.16.0
[6] SummarizedExperiment_1.6.1 DelayedArray_0.2.2 matrixStats_0.52.2 Biobase_2.36.2 GenomicRanges_1.28.1
[11] GenomeInfoDb_1.12.0 IRanges_2.10.0 S4Vectors_0.14.0 BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.10 AnnotationDbi_1.38.0 GenomicAlignments_1.12.0 zlibbioc_1.22.0 BiocParallel_1.10.1 BSgenome_1.44.0
[7] lattice_0.20-35 tools_3.4.0 grid_3.4.0 DBI_0.6-1 digest_0.6.12 Matrix_1.2-10
[13] GenomeInfoDbData_0.99.0 rtracklayer_1.36.0 bitops_1.0-6 biomaRt_2.32.0 RCurl_1.95-4.8 memoise_1.1.0
[19] RSQLite_1.1-2 compiler_3.4.0 GenomicFeatures_1.28.0 XML_3.98-1.7
$ vep --help
#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#
Versions:
ensembl : 88.b8ff470
ensembl-funcgen : 88.3e63130
ensembl-io : 88.277fe7c
ensembl-variation : 88.ed4fefd
ensembl-vep : 88.8
