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Error when importing external blast results #23

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fka21 opened this issue Nov 25, 2021 · 0 comments
Open

Error when importing external blast results #23

fka21 opened this issue Nov 25, 2021 · 0 comments

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@fka21
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fka21 commented Nov 25, 2021

Hello,

I have been using this great package for a while now, but recently something has changed, I could not find out what it was so I ended up writing here for some help.

So I have retrieved all sequences for blasting using phylostratr's algorithm and performed the blasts manually. After that I have formatted the results to be imported(I have attached such an output sample with txt suffix because of github 9925.tab.txt
). After that I tried to import these results, only to get the following error message:

Error in strata_from_taxids(focal_species, taxids, ...) : 
  object 'blastfiles' not found
In addition: Warning message:
In strata_from_taxids(focal_species, taxids, ...) :
  The following subspecies taxa where removed: 100901019510228132806618197451884772323232526712698142792328230128390928788929159300693079723450634508345133762140068242192453514651446704467314683552066610562106239625363596692026956697370707091721772207227723072347240724472457260757476347635765476567719774079558364860376903192179954495979606982399139925

I tried to look into the files, but could not find anything out of order. Do you have any suggestions for a workaround?

Thank you in advance!

Here is the session info:

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] hrbrthemes_0.8.0  wesanderson_0.3.6 reshape2_1.4.4    knitr_1.36        taxizedb_0.3.0    forcats_0.5.1     stringr_1.4.0     dplyr_1.0.7      
 [9] purrr_0.3.4       readr_2.1.0       tidyr_1.1.4       tibble_3.1.6      ggplot2_3.3.5     tidyverse_1.3.1   magrittr_2.0.1    phylostratr_0.2.1

loaded via a namespace (and not attached):
 [1] httr_1.4.2          bit64_4.0.5         jsonlite_1.7.2      modelr_0.1.8        assertthat_0.2.1    BiocManager_1.30.16 rvcheck_0.2.1      
 [8] yulab.utils_0.0.4   blob_1.2.2          cellranger_1.1.0    yaml_2.2.1          gdtools_0.2.3       Rttf2pt1_1.3.9      pillar_1.6.4       
[15] RSQLite_2.2.8       backports_1.3.0     lattice_0.20-45     glue_1.5.0          extrafontdb_1.0     digest_0.6.28       rvest_1.0.2        
[22] colorspace_2.0-2    ggfun_0.0.4         htmltools_0.5.2     plyr_1.8.6          pkgconfig_2.0.3     broom_0.7.10        haven_2.4.3        
[29] patchwork_1.1.1     scales_1.1.1        ggplotify_0.1.0     tzdb_0.2.0          generics_0.1.1      ellipsis_0.3.2      cachem_1.0.6       
[36] withr_2.4.2         cli_3.1.0           crayon_1.4.2        readxl_1.3.1        evaluate_0.14       memoise_2.0.0       fs_1.5.0           
[43] fansi_0.5.0         nlme_3.1-153        xml2_1.3.2          tools_4.0.3         hms_1.1.1           lifecycle_1.0.1     aplot_0.1.1        
[50] munsell_0.5.0       reprex_2.0.1        compiler_4.0.3      systemfonts_1.0.3   gridGraphics_0.5-1  rlang_0.4.12        grid_4.0.3         
[57] rstudioapi_0.13     rappdirs_0.3.3      rmarkdown_2.11      gtable_0.3.0        DBI_1.1.1           curl_4.3.2          R6_2.5.1           
[64] lubridate_1.8.0     extrafont_0.17      fastmap_1.1.0       bit_4.0.4           utf8_1.2.2          hoardr_0.5.2        ape_5.5            
[71] stringi_1.7.5       parallel_4.0.3      Rcpp_1.0.7          vctrs_0.3.8         dbplyr_2.1.1        tidyselect_1.1.1    xfun_0.28
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