zachary-foster
commented
1 year ago Thanks for the report! I do not see this error:
taxize::tax_name("Salicibibacter", get="family", db="ncbi")
#> ══ 1 queries ═══════════════
#>
#> Retrieving data for taxon 'Salicibibacter'
#> ✔ Found: Salicibibacter
#> ══ Results ═════════════════
#>
#> • Total: 1
#> • Found: 1
#> • Not Found: 0
#> db query family
#> 1 ncbi Salicibibacter BacillaceaeCreated on 2023-05-31 with reprex v2.0.2
Does this code work for you? I will need code that reproduces the problem in order to fix it. Sometimes databases have temporary issues not related to taxize, so code that did not work yesterday may work today.
Hi there,
I have a file of genera from some metagenomics sequencing, and I am attempting to use taxize to download higher-level taxonomy data for this file. I create a vector of names (Gnames<-data$names) and then try test<-tax_names(Gnames, get="family", db="ncbi"), which works for a few genera and then seems to always spit a HTTP 400 Error at the same genus in the list (Salicibibacter, taxid 2685905 if that matters!) Any insight as to what I should do would be greatly appreciated- thanks!
R version 4.3.0 (2023-04-21 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22621) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C [5] LC_TIME=English_United States.utf8 time zone: America/New_York tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] taxize_0.9.100 loaded via a namespace (and not attached): [1] crayon_1.5.2 conditionz_0.1.0 nlme_3.1-162 cli_3.6.1 crul_1.4.0 [6] stringi_1.7.12 jsonlite_1.8.4 data.table_1.14.8 zoo_1.8-12 httpcode_0.3.0 [11] triebeard_0.4.1 bold_1.3.0 grid_4.3.0 ape_5.7-1 foreach_1.5.2 [16] compiler_4.3.0 codetools_0.2-19 Rcpp_1.0.10 rstudioapi_0.14 lattice_0.21-8 [21] digest_0.6.31 R6_2.5.1 curl_5.0.0 parallel_4.3.0 urltools_1.7.3 [26] uuid_1.1-0 tools_4.3.0 iterators_1.0.14 xml2_1.3.4
```r ```