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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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can not generate Repeat Landscapes showing TE activity #132

Closed skuri1222 closed 2 months ago

skuri1222 commented 2 months ago

Hi,

Most of the steps run desirably, however I couldn't get the PDF file for Repeat Landscapes showing TE activity. I got the following error message instead. How can I deal with this?

Traceback (most recent call last): File "/home/symbiology/myenv_okabe_shortstack/earlgrey/share/earlgrey-4.4.1-0/scripts//divergenceCalc/divergence_calc.py", line 206, in os.mkdir(args.temp_dir+"/pybedtools/") FileExistsError: [Errno 17] File exists: 'tmp//pybedtools/' Error in dplyr::select(): ! Can't select columns that don't exist. ✖ Column Matches doesn't exist. Backtrace: ▆

  1. ├─... %>% dplyr::rename(family = ID)
  2. ├─dplyr::rename(., family = ID)
  3. ├─dplyr::arrange(., subclass, superfamily, ID)
  4. ├─base::unique(.)
  5. ├─dplyr::select(., -width, -div, -KIMURA80)
  6. ├─dplyr::mutate(...)
  7. ├─dplyr::select(...)
  8. ├─dplyr:::select.data.frame(...)
  9. │ └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
    1. │ └─tidyselect:::eval_select_impl(...)
    2. │ ├─tidyselect:::with_subscript_errors(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ └─tidyselect:::vars_select_eval(...)
    5. │ └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
    6. │ └─tidyselect:::eval_c(expr, data_mask, context_mask)
    7. │ └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
    8. │ └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
    9. │ └─tidyselect:::as_indices_sel_impl(...)
    10. │ └─tidyselect:::as_indices_impl(...)
    11. │ └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
    12. │ └─vctrs::vec_as_location(...)
    13. └─vctrs (local) <fn>()
    14. └─vctrs:::stop_subscript_oob(...)
    15. └─vctrs:::stop_subscript(...)
    16. └─rlang::abort(...)
TobyBaril commented 2 months ago

This is a bug with the new temp directory formatting in the divergence calculation. I am pushing the updates today - apologies!

TobyBaril commented 2 months ago

This has been pushed in v4.4.2, which should go live on bioconda sometime today or tomorrow.