Entering edit mode
Hi,
I'm trying to use ensemblVEP with version 78 of the Ensembl API. It seems that the package doesn't support version 78 yet. Are there any plans to include support for version 78 soon? It seems that a new option that was introduced in version 78 of the API is causing ensemblVEP() to fail. Here is a reproducible example:
fl <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation")
gr <- ensemblVEP(fl)
"@PICK_ORDER" is not exported by the Bio::EnsEMBL::Variation::Utils::VEP module
Can't continue after import errors at /home/mbootwalla/repos/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl line 50.
BEGIN failed--compilation aborted at /home/mbootwalla/repos/ensembl-tools/scripts/variant_effect_predictor/variant_effect_predictor.pl line 67.
Error in .io_check_exists(path(con)) : file(s) do not exist:
'/tmp/RtmpYsB9y8/file2c6244d9bfdd'
Enter a frame number, or 0 to exit
1: ensemblVEP(fl)
2: ensemblVEP(fl)
3: fun(dest, genome = "")
4: fun(dest, genome = "")
5: readVcf(x, "", param = param)
6: readVcf(x, "", param = param)
7: .local(file, genome, param, ...)
8: .readVcf(file, genome, param, row.names = row.names, ...)
9: .scanVcfToVCF(scanVcf(file, param = param, row.names = row.names), file, genome, param)
10: scanVcfHeader(file)
11: scanVcfHeader(file)
12: scanBcfHeader(file, ...)
13: scanBcfHeader(file, ...)
14: Map(function(file, mode) {
bf <- open(BcfFile(file, character(0), ...))
on.exit(close(bf))
scanBc
15: standardGeneric("Map")
16: eval(.dotsCall, env)
17: eval(.dotsCall, env)
18: eval(expr, envir, enclos)
19: .Method(..., f = f)
20: mapply(FUN = f, ..., SIMPLIFY = FALSE)
21: (function (file, mode)
{
bf <- open(BcfFile(file, character(0), ...))
on.exit(close(bf))
scanBcfH
22: open(BcfFile(file, character(0), ...))
23: open.BcfFile(BcfFile(file, character(0), ...))
24: .io_check_exists(path(con))
Output of sessionInfo()
sessionInfo() R version 3.1.2 (2014-10-31) Platform: x86_64-suse-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] ensemblVEP_1.6.0 VariantAnnotation_1.12.4 Rsamtools_1.18.2 Biostrings_2.34.0 [5] XVector_0.6.0 GenomicRanges_1.18.3 GenomeInfoDb_1.2.3 IRanges_2.0.0 [9] S4Vectors_0.4.0 BiocGenerics_0.12.1 BiocInstaller_1.16.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.28.1 base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8 [5] Biobase_2.26.0 BiocParallel_1.0.0 biomaRt_2.22.0 bitops_1.0-6 [9] brew_1.0-6 BSgenome_1.34.0 checkmate_1.5.0 codetools_0.2-9 [13] DBI_0.3.1 digest_0.6.4 fail_1.2 foreach_1.4.2 [17] GenomicAlignments_1.2.1 GenomicFeatures_1.18.2 iterators_1.0.7 RCurl_1.95-4.4 [21] RSQLite_1.0.0 rtracklayer_1.26.2 sendmailR_1.2-1 stringr_0.6.2 [25] tools_3.1.2 XML_3.98-1.1 zlibbioc_1.12.0
Thanks,
Moiz
ensemblVEP is now updated in release (1.6.1) and devel (1.7.1) to include the Ensembl API version 78 flags. These versions should be available via biocLite() Tuesday ~noon PST.
Valerie
Thanks Valerie for adding in support so quickly. I will try updating the packages later today.
It's strange but I restarted my machine and re-ran the above code and everything works fine now. Not sure what I was doing wrong.
I just want to run my setup by you to be sure that what I did in setting up VEP isn't the issue.
I installed the entire Ensembl-API (core, variation, functional, compara modules). Next I installed ensembl-tools which contains VEP. Then I ran the INSTALL.pl script to setup the cache and get the fasta files and then I indexed them using tabix via the provided convert_cache.pl script. I'm working with the GRCh37 cache since my data is still using the hg19 assembly. Next I added the VEP_PATH environmental variable to my .Renviron file so that ensemblVEP can find the variant_effect_predictor.pl script.
Now that the above code was working I tried running VEP in offline mode with the cache and some other options specified and I ran into a new error. It looks like a VEP specific issue but I ran VEP directly with the exact same options and it works. I also tried running it after restarting my RStudio session and also tried running it directly in an R session on the terminal. Not sure what the issue is. The code and the output is as follows:
> param <- VEPParam() > basic(param) <- list(everything=TRUE) > cache(param) <- list(cache=TRUE, dir="$HOME/software/ensembl-VEP", offline=TRUE) > identifier(param) <- list(xref_refseq=TRUE) > colocatedVariants(param) <- list(check_existing=T) > fl <- system.file("extdata", "gl_chr1.vcf", package="VariantAnnotation") > gr <- ensemblVEP(fl, param) 2014-12-23 11:15:39 - Read existing cache info 2014-12-23 11:15:39 - Auto-detected FASTA file in cache directory 2014-12-23 11:15:39 - Checking/creating FASTA index 2014-12-23 11:15:39 - Starting... 2014-12-23 11:15:39 - Detected format of input file as vcf 2014-12-23 11:15:39 - Read 3 variants into buffer 2014-12-23 11:15:39 - Checking for existing variations [> ] [ 0% ] Can't call method "db" on an undefined value at /home/mbootwalla/repos/ensembl-variation/modules/Bio/EnsEMBL/Variation/Utils/VEP.pm line 5888, <GEN1> line 39. Warning message: In is.na(ulst) : is.na() applied to non-(list or vector) of type 'NULL'Thanks,
Moiz