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ConesaLab / SQANTI3

Tool for the Quality Control of Long-Read Defined Transcriptomes
GNU General Public License v3.0
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Error in Pigeon Report Rscript. #236

Closed unique379r closed 7 months ago

unique379r commented 11 months ago

Hi I am trying to make the report out of report Rscript but this gives me the error and the program crashed, any idea ? However, I used "--cage-peak" in pigeon classify.

command:

Rscript $report_pigeon/pigeon_report.R $filt_class $junc_filt $report_pigeon False both

Error:

Error in FUN(X[[i]], ...) : object 'within_cage_peak' not found
Calls: generatePDFreport ... <Anonymous> -> f -> scales_add_defaults -> lapply -> FUN
In addition: Warning messages:
1: Using alpha for a discrete variable is not advised.
2: Using alpha for a discrete variable is not advised.
3: Using alpha for a discrete variable is not advised.
4: Using alpha for a discrete variable is not advised.
Execution halted
almart7 commented 11 months ago

Dear @unique379r please contact @Magdoll for Pigeon related issues. Kind regards!

unique379r commented 9 months ago

Never mind, I found the bug, it pigeon new release > 1.0.0 has changed the name "cage" to "CAGE", which causes the issue to the script.