Pigeon report script fails

[dsampath31]

Operating system MAC

Package name https://github.com/ConesaLab/SQANTI3/blob/master/utilities/report_pigeon/pigeon_report.R Rscript used to provide reports from pigeon, (pigeon 1.1.0)

Conda environment Using Mac's Rstudio server

Describe the bug There is a bug in line 15 in pigeon_report.R script as the number of arguments is 5 not 6. class.file <- args[1] junc.file <- args[2] utilities.path <- args[4] saturation.curves <- args[5] report.format <- args[6]

if (length(args) < 6) { stop("Incorrect number of arguments! Script usage is: [classification file] [junction file] [utilities directory path] [True/False for saturation curves] [pdf|html|both]. Abort!") }

Error message I correct the arguments number and run the script Rscript ~/Documents/isoseq/SQANTI3/utilities/report_pigeon/pigeon_report.R *lite_classification.txt *lite_junctions.txt ~/Documents/isoseq/SQANTI3/utilities/report_pigeon/ False both

`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Warning message:
`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
`summarise()` has grouped output by 'lenCat'. You can override using the `.groups` argument.
Warning message:
`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
Error in `[.data.frame`(t3.a.SJ, , c(1, 5, 6)) :
  undefined columns selected
Calls: rbind ... standardGeneric -> eval -> eval -> eval -> [ -> [.data.frame
Execution halted

[dsampath31]

If I use the unfiltered pigeon classification file, edited the Rscript number of arguments and applied sed "s/within_cage_peak/within_CAGE_peak/g then the script ran fine producing PDF and HTML.

I am wondering why applying the *lite_classification.txt still fails with the error above. Also, the main script requires change in the number of arguments and reflect the latest release with uppercase "CAGE"

[armintoepfer]

Please report to the appropriate repository. We don't maintain SQANTI3