error in 'mutate()'

[raw937]

Warning messages: 1: package ‘ggplot2’ was built under R version 4.3.3 2: package ‘tidyr’ was built under R version 4.3.2 3: package ‘readr’ was built under R version 4.3.2 4: package ‘dplyr’ was built under R version 4.3.2 5: package ‘stringr’ was built under R version 4.3.2 Warning message: One or more parsing issues, call problems() on your data frame for details, e.g.: dat <- vroom(...) problems(dat) Error in mutate(): ℹ In argument: protein_id = ID. Caused by error: ! object 'ID' not found Backtrace: ▆

1. ├─gff %>% mutate(protein_id = ID)
2. ├─dplyr::mutate(., protein_id = ID)
3. ├─dplyr:::mutate.data.frame(., protein_id = ID)
4. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
5. │ ├─base::withCallingHandlers(...)
6. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
7. │ └─mask$eval_all_mutate(quo)
8. │ └─dplyr (local) eval()
9. └─base::.handleSimpleError(<fn>, "object 'ID' not found", base::quote(NULL))
   10. └─dplyr (local) h(simpleError(msg, call))
   11. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) Execution halted [16:31:37] ERROR >> errexit on line 425

Protein_id? Or R error? Thoughts?

[JacksonLab]

Are you using the --gff and --faa input options? If so, I suspect the issue relates to formatting of the gff input. Do the attributes contain an "ID=XYZ123" field that corresponds to the protein ID in the .faa?