problem with feature counts of RNA bulk seq paired data- in Rsubread

Question

I did manage to bild index file (from NCBI transcriptome) and perform alingment in Rsubread in R with my fq files. I did get BAM files as a result and no error. However i am having trouble with next step as featurecount function does not produce any result( 0%). I have tried builtin annotation (hg38)

i am wondering if BAM files are ok..

this is the code i have used

library(Rsubread)
index_path <- "D:/FASTQ_Raw/hum_transcr"
all_files <- list.files(path = "D:/FASTQ_Raw", pattern = ".fq$", full.names = TRUE)
common_prefixes <- unique(gsub("_[12]\\.fq$", "", basename(all_files)))

output_directory <- "aligned_reads/"

dir.create(output_directory, showWarnings = FALSE)

for (prefix in common_prefixes) {
 
  read1_file <- paste0("D:/", prefix, "_1.fq")
  read2_file <- paste0("D:/", prefix, "_2.fq")
  
  output_file <- paste0(output_directory, prefix, "_aligned.bam")
  

  align(index = index_path,
        readfile1 = read1_file,
        readfile2 = read2_file,
        output_file = output_file,
        nthreads = 4)  # Adjust the number of threads as needed
}