Closed rdmorin closed 1 year ago
collated_genome = collate_results(get_gambl_metadata() %>% dplyr::select(sample_id, patient_id, biopsy_id),write_to_file = FALSE,seq_type_filter = "genome",from_cache = TRUE)
/projects/nhl_meta_analysis_scratch/gambl/results_local/shared/gambl_genome_results.tsv
Error in file(con, "rb") : cannot open the connection
In addition: Warning messages:
1: In file(con, "rb") :
'raw = FALSE' but '/projects/rmorin/projects/gambl-repos/gambl-crushton-canary' is not a regular file
2: In file(con, "rb") :
Error in file(con, "rb") : cannot open the connection
The chunk of code specifying the output_file
should be moved to if(from_cache)
. Currently, the code inside if(from_cache)
points to a non-existing file. Unsure how this ended up here. Maybe an unfortunate result of auto-merge. After these paths have been updated to point to shared/gambl{seq_type_filter}results.tsv the function runs as expected with from_cache = TRUE
.
The issue with this parameter is that one of the collate functions,collate_curated_sv_results
is trying to do a left_join
for one of the files (genome_EBV_status) but no common variables are available. i.e the sample_id
column in genome_EBV_status.tsv is called sample
. Not possible to specify by = c("sample_id" = "sample")
, since this is causing an error for the other curated SV results files.
Looking into an alternative solution.
Causing error in dplyr::left_join (collate_curated_sv_results)
Error in `left_join()` at GAMBLR/R/utilities.R:1541:4:
`by` must be supplied when `x` and `y` have no common variables.
use by = character()` to perform a cross-join.
This issue is being addressed in this PR
Can you please add the code you're running to test each use case?
I can't seem to get collate_results to generate the cached outputs nor can I get it to load the cached result. If I specify from_cache = T it still loads the mutations as if it's ignoring that option completely. This really needs to be addressed.