GBCounts gives no hit to all junction counts rows

[hkarakurt8742]

Hello,
I am using ASPli for a dataset with 94 FASTQ files (scRNA-Seq with Smart-Seq2 full transcript). I used STAR for alignment and build all required dataset based on the same genome version.

When I run gbCounts with this code,

gbcounts <- gbCounts(features=features, targets=targets, minReadLength = 28, maxISize = 50000 , libType = "SE")

gbcounts@junction.counts section is full of zeros and looks like this:

junction gene strand multipleHit symbol gene_coordinates bin_spanned j_within_bin
1.90050.90287 noHit noHit * - - - - -
1.91629.92091 noHit noHit * - - - - -
1.120869.120874 noHit noHit * - - - - -
1.155831.164263 noHit noHit * - - - - -
1.180569.180902 noHit noHit * - - - - -
1.185350.185491 noHit noHit * - - - - -
1.268204.268667 noHit noHit * - - - - -
1.357586.358049 noHit noHit * - - - - -
1.378590.380475 noHit noHit * - - - - -

What might be the problem. Minimum read length in my BAM files is 28 so I used it, chromosome notations are same with GTF and Fasta file. I used ASPli before but it never happened.

Thank you in advance.