I am getting an error while running the proActiv function in my Promoter Finding program.

Ive never encountered this issue before, but this is a new set of junction files. I have checked that my genome used for preparePromoterAnnotation does match up with the alignment genome. The condition counts do match the junction file counts, and all junction files contain at least some non-zero entries.

Any help is appreciated.

The error in question:

Error in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  : 
  every gene contains at least one zero, cannot compute log geometric means
In addition: There were 22 warnings (use warnings() to see them)

The code producing it:

library(proActiv)

setwd("~/Desktop/PromoterFinding/Bulk")

brain_file_names <- list.files("~/Desktop/brain_alignment/")[grep("SJ.out.tab", list.files("~/Desktop/brain_alignment/"))]
heart_file_names <- list.files("~/Desktop/heart_alignment/")[grep("SJ.out.tab", list.files("~/Desktop/heart_alignment/"))]
spleen_file_names <- list.files("~/Desktop/spleen_alignment/")[grep("SJ.out.tab", list.files("~/Desktop/spleen_alignment/"))]
liver_file_names <- list.files("~/Desktop/liver_alignment/")[grep("SJ.out.tab", list.files("~/Desktop/liver_alignment/"))]

files <- list.files("~/Desktop/PromoterFinding/Bulk")[grep("SJ.out.tab", list.files("~/Desktop/PromoterFinding/Bulk"))]

condition_1 <- rep(c('Brain'), each=86)
condition_2 <- rep(c('Heart'), each=56)
condition_3 <- rep(c('Liver'), each=39)
condition_4 <- rep(c('Spleen'), each=32)
condition <- c(condition_1,condition_2,condition_3,condition_4)

promoterAnnotation <- preparePromoterAnnotation(file = '~/Desktop/PromoterFinding/Homo_sapiens.GRCh38.110.chr.gtf.gz',
                                                species = 'Homo_sapiens')

head(promoterAnnotation@promoterCoordinates)
names(GenomeInfoDb::genomeStyles())

result <- proActiv(files = files, 
                   promoterAnnotation = promoterAnnotation,
                   condition = condition)
show(result)