Question: problem using ensemblVEP with GRC37
0
gravatar for mikko.arvas
2.0 years ago by
mikko.arvas0 wrote:

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

 

ensemblvep grch37 • 587 views
ADD COMMENTlink written 2.0 years ago by mikko.arvas0
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