Off topic:RNA-seq from Nanopore featureCounts

Question

[v.shapovalova1]

Hello,

I have RNA-seq reads from Nanopore(kit RNA002, U-based fastq), I aligned them with minimap2 and tried to count with featureCounts. The reference was transcriptome from https://www.gencodegenes.org/human/. my command was

 fc<- Rsubread::featureCounts(files="aln.bam",annot.inbuilt="hg38",isLongRead="True")

 Process BAM file aln.bam...                                                ||
||    Single-end reads are included.                                          ||
||    Total alignments : 2081002                                              ||
||    **Successfully assigned alignments : 0 (0.0%)**                             ||
||    Running time : 0.26 minutes   
**Warning message:
In paste("readSummary", ann, files_C, fout, as.numeric(isPairedEnd),  :
  NAs introduced by coercion**

I checked my bam file and have such a statistics:

SN raw total sequences: 632940
SN filtered sequences: 0
SN sequences: 632940
SN is sorted: 1
SN 1st fragments: 632940
SN last fragments: 0
SN reads mapped: 609258
SN reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
SN reads unmapped: 23682

What could it be?

A lot of thanks.