Hello,

I'm currently experiencing a problem with the my variant package. When I run the :

inputvariant_patho <- getVariants(inputhgvs, 
                                        fields = c("query", "notfound", "dbnsfp",
                                                   "cadd.rawscore", "cadd.phred",
                                                   "cadd.phast_cons.primate","cadd.phast_cons.mammalian", 
                                                   "cadd.phast_cons.vertebrate",
                                                   "cadd.phylop.primate", 
                                                   "cadd.phylop.mammalian", "cadd.phylop.vertebrate"))

I get this error message:

Error in .request.post(myvariant = myvariant, path, params = params.i) : Request returned unexpected status code: Response [http://myvariant.info/v1/variant/] Date: 2025-03-03 15:09 Status: 500 Content-Type: text/html Size: 186 B

500 Internal Server Error

It worked before, I don't understand what's going on.

sessionInfo( )

R version 4.4.2 (2024-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale: [1] LC_COLLATE=French_France.utf8 LC_CTYPE=French_France.utf8 LC_MONETARY=French_France.utf8 [4] LC_NUMERIC=C LC_TIME=French_France.utf8

time zone: Europe/Paris tzcode source: internal

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

other attached packages: [1] reshape2_1.4.4 venn_1.12 vcfR_1.15.0 lubridate_1.9.4
[5] forcats_1.0.0 purrr_1.0.4 readr_2.1.5 tidyr_1.3.1
[9] tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0 dplyr_1.1.4
[13] kableExtra_1.4.0 rtracklayer_1.66.0 stringr_1.5.1 plyr_1.8.9
[17] myvariant_1.36.0 VariantAnnotation_1.52.0 Rsamtools_2.22.0 Biostrings_2.74.1
[21] XVector_0.46.0 SummarizedExperiment_1.36.0 Biobase_2.66.0 GenomicRanges_1.58.0
[25] GenomeInfoDb_1.42.3 IRanges_2.40.1 S4Vectors_0.44.0 MatrixGenerics_1.18.1
[29] matrixStats_1.5.0 BiocGenerics_0.52.0 xlsx_0.6.5

loaded via a namespace (and not attached): [1] splines_4.4.2 later_1.4.1 BiocIO_1.16.0 bitops_1.0-9
[5] XML_3.99-0.18 rpart_4.1.24 lifecycle_1.0.4 lattice_0.22-6
[9] MASS_7.3-64 backports_1.5.0 magrittr_2.0.3 Hmisc_5.2-2
[13] sass_0.4.9 rmarkdown_2.29 jquerylib_0.1.4 yaml_2.3.10
[17] remotes_2.5.0 httpuv_1.6.15 sessioninfo_1.2.3 pkgbuild_1.4.6
[21] DBI_1.2.3 abind_1.4-8 pkgload_1.4.0 zlibbioc_1.52.0
[25] RCurl_1.98-1.16 nnet_7.3-20 xlsxjars_0.6.1 GenomeInfoDbData_1.2.13 [29] vegan_2.6-10 svglite_2.1.3 permute_0.9-7 codetools_0.2-20
[33] DelayedArray_0.32.0 xml2_1.3.6 tidyselect_1.2.1 UCSC.utils_1.2.0
[37] memuse_4.2-3 farver_2.1.2 base64enc_0.1-3 webshot_0.5.5
[41] GenomicAlignments_1.42.0 jsonlite_1.9.0 ellipsis_0.3.2 pinfsc50_1.3.0
[45] Formula_1.2-5 systemfonts_1.2.1 tools_4.4.2 Rcpp_1.0.14
[49] glue_1.8.0 gridExtra_2.3 SparseArray_1.6.1 xfun_0.51
[53] mgcv_1.9-1 admisc_0.37 usethis_3.1.0 withr_3.0.2
[57] BiocManager_1.30.25 fastmap_1.2.0 digest_0.6.37 timechange_0.3.0
[61] R6_2.6.1 mime_0.12 colorspace_2.1-1 RSQLite_2.3.9
[65] generics_0.1.3 data.table_1.16.4 httr_1.4.7 htmlwidgets_1.6.4
[69] S4Arrays_1.6.0 pkgconfig_2.0.3 rJava_1.0-11 gtable_0.3.6
[73] blob_1.2.4 htmltools_0.5.8.1 profvis_0.4.0 scales_1.3.0
[77] png_0.1-8 knitr_1.49 rstudioapi_0.17.1 tzdb_0.4.0
[81] rjson_0.2.23 checkmate_2.3.2 nlme_3.1-167 curl_6.2.1
[85] cachem_1.1.0 parallel_4.4.2 miniUI_0.1.1.1 foreign_0.8-88
[89] AnnotationDbi_1.68.0 restfulr_0.0.15 pillar_1.10.1 grid_4.4.2
[93] vctrs_0.6.5 urlchecker_1.0.1 promises_1.3.2 xtable_1.8-4
[97] cluster_2.1.8 htmlTable_2.4.3 evaluate_1.0.3 tinytex_0.55
[101] GenomicFeatures_1.58.0 cli_3.6.4 compiler_4.4.2 rlang_1.1.5
[105] crayon_1.5.3 labeling_0.4.3 fs_1.6.5 stringi_1.8.4
[109] viridisLite_0.4.2 BiocParallel_1.40.0 munsell_0.5.1 devtools_2.4.5
[113] Matrix_1.7-2 BSgenome_1.74.0 hms_1.1.3 bit64_4.6.0-1
[117] KEGGREST_1.46.0 shiny_1.10.0 memoise_2.0.1 bslib_0.9.0
[121] bit_4.5.0.1 ape_5.8-1

You don't show anything about the data you are annotating, so it's hard to say what the problem might be. Does the example data work for you?

> example("getVariants")

gtVrnt> ## given a list of HGVS ids
gtVrnt> vars <- c('chr1:g.866422C>T',
gtVrnt+ 'chr1:g.876664G>A',
gtVrnt+ 'chr1:g.69635G>C',
gtVrnt+ 'chr1:g.69869T>A',
gtVrnt+ 'chr1:g.881918G>A',
gtVrnt+ 'chr1:g.865625G>A',
gtVrnt+ 'chr1:g.879368C>A',
gtVrnt+ 'chr1:g.889226C>T',
gtVrnt+ 'chr1:g.879492C>G',
gtVrnt+ 'chr1:g.879423T>G',
gtVrnt+ 'chr1:g.881602C>T',
gtVrnt+ 'chr1:g.879115C>G',
gtVrnt+ 'chr1:g.69892T>C',
gtVrnt+ 'chr1:g.879381C>T',
gtVrnt+ 'chr1:g.878330C>G')

gtVrnt> ## Return the list of variant object for the given list of HGVS ids.
gtVrnt> df <- getVariants(vars, fields="dbsnp, wellderly")
Concatenating data, please be patient.
> dim(df)
[1] 15 23

And if I use the example data with your query it still works:

> df2 <- getVariants(vars, fields = c("query", "notfound", "dbnsfp",
                                                   "cadd.rawscore", "cadd.phred",
                                                   "cadd.phast_cons.primate","cadd.phast_cons.mammalian", 
                                                   "cadd.phast_cons.vertebrate",
                                                   "cadd.phylop.primate", 
                                                   "cadd.phylop.mammalian", "cadd.phylop.vertebrate"))
. + Concatenating data, please be patient.
> dim(df2)
[1]  15 306

There are two possibilities. First, your variants may be problematic in some way, which is causing an error on the myvariants.info server. Second, there may have been an intermittent issue at myvariants.info that caused your query to fail, and simply re-running may now work.