[BUG] fatal error in SQANTI3_report.R

[diekhans]

Is there an existing issue for this?

• I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• I have loaded the SQANTI3.env conda environment

Problem description

SQANTI3_report.R fails with. cryptic error:

Error in `[.data.frame`(t3.a.SJ, , c(1, 5, 6)) :
  undefined columns selected
Calls: rbind ... standardGeneric -> eval -> eval -> eval -> [ -> [.data.frame
Execution halted

Code sample

data files and script to reproduce the problem are here

https://hgwdev.gi.ucsc.edu/~markd/crg/crg-sqanti-err.tar.gz

data and script to do the full squant3 run is here

https://hgwdev.gi.ucsc.edu/~markd/crg/crg-sqanti-err-full.tar.gz

Error

Error in [.data.frame(t3.a.SJ, , c(1, 5, 6)) :
undefined columns selected
Calls: rbind ... standardGeneric -> eval -> eval -> eval -> [ -> [.data.frame
Execution halted

Anything else?

No response

[alexpan00]

Hi,

I think I have suffered this error myself before, it was caused by not having any transcript with non-canonical junctions. This also happens in the classification file you have provided.

Thanks for reporting this bug,
Alejandro.

[TianYuan-Liu]

Hi,

I think I have suffered this error myself before, it was caused by not having any transcript with non-canonical junctions. This also happens in the classification file you have provided.

Thanks for reporting this bug, Alejandro.

Hi Alejandro, thanks for reporting this bug and sharing your experience. I'll address this issue related to transcripts with non-canonical junctions in the R report to prevent future occurrences. Your input is invaluable in improving our processes.

[carolinamonzo]

This error has now been fixed in v5.2.1. Thank you Mark and Tian!