error using ensemblVEP v88 when querying rs67418256 with basic(param_vep)$everything=TRUE
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mlrubio • 0
@mlrubio-13065
Last seen 3.9 years ago

Hi to all,

When I use ensemblVEP with vep v88  (Running under: Ubuntu 16.04.2 LTS and bioconductor 3.5) to query rs67418256  and VEPParam():

suppressMessages(library(ensemblVEP))
write("rs67418256", file = "example.txt")

param_vep <- VEPParam()
basic(param_vep)$verbose = FALSE
basic(param_vep)$everything=TRUE
database(param_vep)$host = "ensembldb.ensembl.org"
database(param_vep)$database = FALSE
cache(param_vep)$cache = TRUE

ensemblVEP(file = "example.txt", param = param_vep)

I obtain the following error:

2017-05-16 19:45:01 - INFO: Database will be accessed when using --hgvs
Error: scanVcf: _DNAencode(): invalid DNAString input character: ')' (byte value 41)
  path: /tmp/RtmpvQCmLN/file621b81eef23

With traceback:

> traceback()
18: stop("scanVcf: ", conditionMessage(err), "\n  path: ", file,
        call. = FALSE)
17: value[[3L]](cond)
16: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
        names[nh], parentenv, handlers[[nh]])
15: tryCatchList(expr, classes, parentenv, handlers)
14: tryCatch({
        file <- normalizePath(path.expand(file))
        if (!file.exists(file))
            stop("file does not exist")
        maps <- .vcf_scan_header_maps(file, fixed, info, geno, samples,
            ...)
        result <- .Call(.scan_vcf_character, file, as.integer(yieldSize),
            maps$samples, maps$fmap, maps$imap, maps$gmap, row.names)
        setNames(result, "*:*-*")
    }, scanTabix_io = function(err) {
        stop("scanVcf: ", conditionMessage(err), call. = FALSE)
    }, error = function(err) {
        stop("scanVcf: ", conditionMessage(err), "\n  path: ", file,
            call. = FALSE)
    })
13: .vcf_scan_character(file, ..., fixed = vcfFixed(param), info = vcfInfo(param),
        geno = vcfGeno(param), samples = vcfSamples(param))
12: scanVcf(file, param = param, row.names = row.names, ...)
11: scanVcf(file, param = param, row.names = row.names, ...)
10: .scanVcfToVCF(scanVcf(file, param = param, row.names = row.names,
        ...), file, genome, param)
9: .readVcf(file, genome, param, row.names = row.names, ...)
8: .local(file, genome, param, ...)
7: readVcf(x, "", param = param)
6: readVcf(x, "", param = param)
5: .local(x, VCFRowID, ...)
4: fun(dest, genome = "")
3: fun(dest, genome = "")
2: ensemblVEP(file = "example.txt", param = param_vep)
1: ensemblVEP(file = "example.txt", param = param_vep)

 

When I run vep from the command line (in the same system) with the option --everything I obtain the following result:

rs67418256    6:132376504-132376826    -    ENSG00000079931    ENST00000336749    Transcript    upstream_gene_variant    -    -    -    -    -    -    IMPACT=MODIFIER;DISTANCE=1439;STRAND=-1;VARIANT_CLASS=deletion;SYMBOL=MOXD1;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC:21063;BIOTYPE=protein_coding;TSL=1;ENSP=ENSP00000336998;SWISSPROT=Q6UVY6;UNIPARC=UPI000013D392
rs67418256    6:132376504-132376826    -    ENSG00000079931    ENST00000367963    Transcript    intron_variant    -    -    -    -    -    -    IMPACT=MODIFIER;STRAND=-1;VARIANT_CLASS=deletion;SYMBOL=MOXD1;SYMBOL_SOURCE=HGNC;HGNC_ID=HGNC:21063;BIOTYPE=protein_coding;CANONICAL=YES;TSL=1;APPRIS=P1;CCDS=CCDS5152.2;ENSP=ENSP00000356940;SWISSPROT=Q6UVY6;UNIPARC=UPI000003F04F;INTRON=1/11;HGVSc=ENST00000367963.7:c.265-2049_265-1727delAAGAAGCTGTAGTTGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAAAACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAA

Best regards

Miguel Rubio

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] ensemblVEP_1.16.0          VariantAnnotation_1.22.0
 [3] Rsamtools_1.28.0           Biostrings_2.44.0
 [5] XVector_0.16.0             SummarizedExperiment_1.6.1
 [7] DelayedArray_0.2.2         matrixStats_0.52.2
 [9] Biobase_2.36.2             GenomicRanges_1.28.1
[11] GenomeInfoDb_1.12.0        IRanges_2.10.1
[13] S4Vectors_0.14.1           BiocGenerics_0.22.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10             AnnotationDbi_1.38.0     GenomicAlignments_1.12.1
 [4] 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
[10] 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
[16] 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
[22] XML_3.98-1.7
>
ensemblvep • 540 views
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