countFeatures() from bam files giving 0% alignment

[marykthompson]

I am trying to use countFeatures() with my bam files to use diffUTR. Unfortunately, it says that 0% are aligned and when I go to the next step that causes an error. I have checked that Rsubread::featureCounts can produce alignments with the bam files. Here my specific code:

ah <- AnnotationHub()
ahid <- query(ah, c("EnsDb", "Drosophila melanogaster", 99))$ah_id[1]
ensdb <- ah[[ahid]]
bins <- prepareBins(ensdb)

bamfiles <- file.path(bam_dir, c("input_1-rep1.sample.bam"))
rse <- countFeatures(bamfiles, bins, strandSpecific=1, readLength=80, nthreads=6, isPairedEnd=TRUE)

Interestingly, the example on page 3 of the diffUTR manual produces the same problem (0% alignment). I don't know if this could be related?

data("example_gene_annotation", package="diffUTR")
bins <- prepareBins(example_gene_annotation)
bam_files <- list.files(system.file("extdata", package="diffUTR"),
                        pattern="bam$", full=TRUE)
se <- countFeatures(bam_files, bins, verbose=FALSE)

Any ideas what is going wrong? I am running diffUTR v1.3.0. I went through the vignette with the preloaded analysis and everything looked good. Would be great to use the package on my data. Thanks!