Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Regarding R2Dtool metafeature plots #8

Open
PRIYANKA-22091995 opened this issue Dec 27, 2024 · 0 comments
Open

Regarding R2Dtool metafeature plots #8

PRIYANKA-22091995 opened this issue Dec 27, 2024 · 0 comments

Comments

@PRIYANKA-22091995
Copy link

Hi,
I was trying to run the R2Dtool, the r2d liftover and r2d annotation work fine for me. However, when I try to run the r2d plotMetaTranscript script I get the following error:
Command used:
./r2d plotMetaTranscript -i "/home/priyanka/R2D_m6a_Cheui_PvSal1/annotatetrial.bed" -o "/home/priyanka/R2D_m6a_Cheui_PvSal1/metatranscript_m6A.png" --filter-field "stoichiometry" --cutoff "1" --cutoff-type "lower" -l
Error:
Arguments being passed to R2_plotMetaTranscript.R:
Rscript R2_plotMetaTranscript.R /home/priyanka/R2D_m6a_Cheui_PvSal1/annotatetrial.bed /home/priyanka/R2D_m6a_Cheui_PvSal1/metatranscript_m6A.png stoichiometry 1 lower -c loess -l
Executing R script: "/home/priyanka/R2Dtool/target/release/../../scripts/R2_plotMetaTranscript.R"
R script stdout:
[1] "Using loess method for confidence intervals."

R script stderr:
Parsed with column specification:
cols(
.default = col_double(),
transcript = col_character(),
name = col_character(),
score = col_character(),
strand = col_character(),
motif = col_character(),
gene_id = col_character(),
gene_name = col_logical(),
transcript_biotype = col_logical(),
cds_start = col_logical(),
cds_end = col_logical(),
tx_end = col_logical(),
transcript_metacoordinate = col_logical(),
abs_cds_start = col_logical(),
abs_cds_end = col_logical()
)
See spec(...) for full column specifications.
Warning message:
guess_max is a very large value, setting to 21474836 to avoid exhausting memory
Error in mutate():
ℹ In argument: interval = cut(...).
Caused by error in cut.default():
! 'x' must be numeric
Backtrace:

  1. ├─global compute_ratio(calls, ci_method)
  2. │ └─... %>% mutate(ratio = sig / (sig + ns + 1e-09))
  3. ├─dplyr::mutate(., ratio = sig/(sig + ns + 1e-09))
  4. ├─tidyr::pivot_wider(...)
  5. │ └─tidyr::build_wider_spec(...)
  6. │ ├─tidyselect::vars_select(tbl_vars(data), !!enquo(names_from))
  7. │ │ └─tidyselect:::eval_select_impl(...)
  8. │ └─dplyr::tbl_vars(data)
  9. │ ├─dplyr:::new_sel_vars(tbl_vars_dispatch(x), group_vars(x))
  10. │ │ └─base::structure(...)
  11. │ └─dplyr:::tbl_vars_dispatch(x)
  12. ├─dplyr::summarise(., n = n(), .groups = "drop")
  13. ├─dplyr::group_by(., interval, filter)
  14. ├─dplyr::mutate(...)
  15. ├─dplyr:::mutate.data.frame(...)
  16. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
  17. │ ├─base::withCallingHandlers(...)
  18. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
  19. │ └─mask$eval_all_mutate(quo)
  20. │ └─dplyr (local) eval()
  21. ├─base::cut(...)
  22. ├─base::cut.default(...)
  23. │ └─base::stop("'x' must be numeric")
  24. └─base::.handleSimpleError(...)
  25. └─dplyr (local) h(simpleError(msg, call))
  26. └─rlang::abort(message, class = error_class, parent = parent, call = error_call)
    

Execution halted

Error: R script exited with non-zero status: ExitStatus(unix_wait_status(256))
PlotMetaTranscript generation failed. Please check the error messages above.

Please let me know what could went wrong.
Thank you in advance.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant