search

annadalmolin / CRAFT

CRAFT is a computational pipeline that predicts circRNA sequence and molecular interactions with miRNAs and RBPs, along with their coding potential. CRAFT provides a comprehensive graphical visualization of the results, links to several knowledge databases, extensive functional enrichment analysis and combination of predictions for different circRNAs. CRAFT is a useful tool to help the user explore the potential regulatory networks involving the circRNAs of interest and generate hypotheses about the cooperation of circRNAs into the regulation of biological processes.
Other
8 stars 2 forks source link

Error: CircRNA Sequences Provided by User Not Completing Predictions #4

Open mlvanhorn opened 1 year ago

mlvanhorn commented 1 year ago

Hello,

I was able to get CRAFT to complete when having it perform the sequence extraction for me. However, I am running into completion issues when providing CRAFT with the circRNA sequences.

When processing the individual circRNAs, I get this error for two of them.

  |...........................................................           |  84%
label: disease_association_RBP (with options) 
List of 2
 $ echo   : logi FALSE
 $ include: logi FALSE

Please wait we are processing your accessions ...

Error in file(file, ifelse(append, "a", "w")) :                               
  all connections are in use
Calls: <Anonymous> ... <Anonymous> -> signalCondition -> <Anonymous> -> cat -> file
In addition: There were 50 or more warnings (use warnings() to see the first 50)

Execution halted
mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory

For the last circRNA prediction, I get this error in the same location, at 84%. 

Please wait we are processing your accessions ...
Quitting from lines 2772-2830 (functional_predictions_single_circRNA.Rmd)     
Error: Can't subset columns that don't exist.
x Column `Involvement.in.disease` doesn't exist.
Backtrace:
     x
  1. +-rmarkdown::render(...)
  2. | \-knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  3. |   \-knitr:::process_file(text, output)
  4. |     +-base::withCallingHandlers(...)
  5. |     +-knitr:::process_group(group)
  6. |     \-knitr:::process_group.block(group)
  7. |       \-knitr:::call_block(x)
  8. |         \-knitr:::block_exec(params)
  9. |           \-knitr:::eng_r(options)
 10. |             +-knitr:::in_dir(...)
 11. |             \-knitr:::evaluate(...)
 12. |               \-evaluate::evaluate(...)
 13. |                 \-evaluate:::evaluate_call(...)
 14. |                   +-evaluate:::timing_fn(...)
 15. |                   +-base:::handle(...)
 16. |                   +-base::withCallingHandlers(...)
 17. |                   +-base::withVisible(eval(expr, envir, enclos))
 18. |                   \-base::eval(expr, envir, enclos)
 19. |                     \-base::eval(expr, envir, enclos)
 20. \-UniprotR::Get.diseases(PathologyObj)
 21.   +-dplyr::select(Pathology_object, "Involvement.in.disease")
 22.   \-dplyr:::select.data.frame(Pathology_object, "Involvement.in.disease")
 23.     \-tidyselect::eval_select(expr(c(...)), .data)
 24.       \-tidyselect:::eval_select_impl(...)
 25.         +-tidyselect:::with_subscript_errors(...)
 26.         | +-base::tryCatch(...)
 27.         | | \-base:::tryCatchList(expr, classes, parentenv, handlers)
 28.         | |   \-base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 29.         | |     \-base:::doTryCatch(return(expr), name, parentenv, handler)
 30.         | \-tidyselect:::instrument_base_errors(expr)
 31.         |   \-base::withCallingHandlers(...)
 32.         \-tidyselect:::vars_select_eval(...)
 33.           \-tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 34.             \-tidyselect:::eval_c(expr, data_mask, context_mask)
 35.               \-tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 36.                 \-tidyselect:::walk_data_tree(new, data_mask, context_mask)
 37.                   \-tidyselect:::as_indices_sel_impl(...)
 38.                     \-tidyselect:::as_indices_impl(x, vars, strict = strict)
 39.                       \-tidyselect:::chr_as_locations(x, vars)
 40.                         \-vctrs::vec_as_location(x, n = length(vars), names = vars)
 41.                           \-(function () ...
 42.                             \-vctrs:::stop_subscript_oob(...)
 43.                               \-vctrs:::stop_subscript(...)
There were 50 or more warnings (use warnings() to see the first 50)

Execution halted
mv: cannot stat 'functional_predictions_single_circRNA.html': No such file or directory

The final prediction generating thefunctional_predictions_all_circRNA.htmland functional_predictions_all_circRNA.knit.md finishes completely with no errors.

I also get this error at the beginning of the run about permission denied to access .mature_hsa.fa. I checked my input files and I don't have this file in my inputs. 

Putative sequence/s already extracted or provided by the user.
/scripts/pipeline_predictions.sh: line 102: /data/input/.mature_hsa.fa: Permission denied
MiRNA binding site prediction analysis already performed.
RBP binding site prediction analysis already performed.

Any help would be greatly appreciated. Thank you for your time.

Best,

Megan