Error: CircRNA Sequences Provided by User Not Completing Predictions

[mlvanhorn]

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