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brendanf / rITSx

Extract ITS and Neighboring Regions from Eukaryotic DNA Sequences
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error on Rstudio #1

Open AnneJRomero opened 2 weeks ago

AnneJRomero commented 2 weeks ago

Hi,

I have followed the installation steps on here and am trying to get this to work on RStudio but I get the following errors when I try and run the test.fasta.

test <- readDNAStringSet("test.fasta", format = "fasta")

itsx( test, out_root = tempfile("itsx"), taxon = "fungi", e_value = 1e-05, s_value = 0, n_value = 2, selection_priority = c("score", "sum", "domains", "eval"), search_eval = 0.05,

search_score = NULL,

allow_single_domain = c(1e-09, 0), allow_reorder = FALSE, complement = TRUE,

cpu = 1,

multi_thread = cpu > 1,

heuristics = FALSE, nhmmer = FALSE, summary = TRUE, graphical = TRUE, fasta = TRUE, preserve = FALSE, save_regions = c("ITS1", "ITS2", "5.8S"), anchor = 0, require_anchor = 0, only_full = FALSE, partial = 0, concat = FALSE, minlen = 0, positions = TRUE, table = FALSE, detailed_results = FALSE, not_found = TRUE, truncate = TRUE, silent = FALSE, graph_scale = 0, save_raw = FALSE, read_function = FALSE )

Error in glue_data(.x = NULL, ..., .sep = .sep, .envir = .envir, .open = .open, : Expecting '}'

I would appriciate your help. Thank you.

brendanf commented 2 weeks ago

I believe I fixed this now with f8950c89. Can you please test with the latest github version (i.e., remotes::install_github("brendanf/rITSx"))

AnneJRomero commented 2 weeks ago

Hi, thank you for your quick reply. I got a new error below

Error in itsx(test, out_root = tempfile("itsx"), taxon = "fungi", e_value = 1e-05, : ITSx failed with return code 127.

brendanf commented 2 weeks ago

That sounds like a problem finding the ITSx script. What operating system are you using and how did you install ITSx?

AnneJRomero commented 2 weeks ago

I have Microsoft windows, and using the Rstudio Desktop.

brendanf commented 2 weeks ago

Did you download ITSx and install it?

AnneJRomero commented 2 weeks ago

I have downloaded it (with the files below) but I'm not sure how to install it?

image

brendanf commented 2 weeks ago

I realize now that it is probably difficult to use ITSx (and therefore rITSx) on Windows, because it uses Hmmer internally, and according to the Hmmer documentation, it cannot be installed directly in Windows. They mention using the Linux subsystem for Windows, but I am unfortunately not qualified to give advice about how to do that in practice, or how to access it from R running in Windows (alternatively, how to run R studio inside the Linux subsystem). Sorry!

As an alternative, I think you can run ITSx online in PlutoF, and that PipeCraft can run it in Windows using Docker containers.

AnneJRomero commented 1 week ago

Thank you so much for your help :)