repcred failure on processing alleles

airr-community / rep-cred

SW Tools Group - Repertoire Credibility Tool

Creative Commons Attribution 4.0 International

0 stars 3 forks source link

repcred failure on processing alleles #27

Closed bcorrie closed 7 months ago

bcorrie commented 9 months ago

Creating a set of issues as I try repertoires from a bunch of different studies.

PRJNA752617, repertoire_id = 613b7f3eadf6058ccd849076 on covid19-1.ireceptor.org

Rendering book in directory '.'

processing file: _main.Rmd
Quitting from lines 258-279 (_main.Rmd) 
Error in dplyr::summarise(., frequency = sum(!!as.name("proportion")),  : 
  â„¹ In argument: `unique_alleles = paste0(...)`.
Caused by error in `strsplit()`:
! non-character argument
Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted

bcorrie commented 9 months ago

Good news is, no errors on study_id = E-MTAB-9995 and study_id = PRJNA731610 for the repertoires I tested.

bcorrie commented 9 months ago

study_id = PRJNA715378 also fails with this error.

Both PRJNA715378 and PRJNA752617 from the same group/author, probably the same annotation tool/problem.

bcorrie commented 9 months ago

This is what a failed output looks like...

williamdlees commented 9 months ago

Brian this is enormously useful, thanks!On 15 Feb 2024, at 23:05, Brian Corrie @.***> wrote: Creating a set of issues as I try repertoires from a bunch of different studies. PRJNA752617, repertoire_id = 613b7f3eadf6058ccd849076 on covid19-1.ireceptor.org Rendering book in directory '.'

processing file: _main.Rmd Quitting from lines 258-279 (_main.Rmd) Error in dplyr::summarise(., frequency = sum(!!as.name("proportion")), : â„¹ In argument: unique_alleles = paste0(...). Caused by error in strsplit(): ! non-character argument Calls: tryCatch -> tryCatchList -> tryCatchOne -> Execution halted

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>

bcorrie commented 7 months ago

This one appears to be still failing with a new error. This is true on:

Repertoire ID: 613b7f3eadf6058ccd849076 Repertoire ID: 609e9b5f8a4ef25782e2103e

processing file: _main.Rmd
Quitting from lines 185-228 (_main.Rmd)
Error in `dplyr::mutate()`:
ℹ In argument: `vj_not_frame = !vj_in_frame`.
Caused by error:
! object 'vj_in_frame' not found
Backtrace:
1. ... %>% ...
7. dplyr:::mutate.data.frame(...)
8. dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
10. dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
11. mask$eval_all_mutate(quo)
12. dplyr (local) eval()
Execution halted

Looks like failure if missing vj_in_frame data.

ssnn-airr commented 7 months ago

@bcorrie can you please update your repcred and test these repertoires again?

bcorrie commented 7 months ago

Yes, both of these are now working...