Why is there no assigned gene when the sequence can be completely aligned

[pandh0607]

Hi Alex,
Here's an example of one read with such a result.
R1:
@A00199:1025:HCCFMDSXC:4:1233:8956:32597 1:N:0:TCGCCTTA+CTAGCGCT
ACAGCAGAAGGCCAGAGCATTCGATCCACGTGCTTGAGCACTTCGATTTGTGGGACAGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGGCCTCGGTGGGGCCCAGTTATAAGAAAAGCGGTGAGGACCAAATACAAAAAGGAAAT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:,,F,,,,,,FF,:,:,F::,,,F,:F,F,:::,,,,::,,,,,,,:,FFF,,,,F,,

R2:
@A00199:1025:HCCFMDSXC:4:1233:8956:32597 2:N:0:TCGCCTTA+CTAGCGCT
TTTTGGAAGTGGTCCAGACCGCTGTTCTGATAACTGTGGCCCTCCGAGGG
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

ref fasta:

chr1003 1003
TTTTGGAAGTGGTCCAGACCGCTGTTCTGATAACTGTGGCCCTCCGAGGG

gtf:
chr1003 HAVANA exon 1 50 . + . gene_id "ENSG00000101199"; transcript_id "c77eb74"; gene_name "ARFGAP1"

bam:
A00199:1025:HCCFMDSXC:4:1233:8956:32597 0 chr1003 1 255 50M * 0 0 TTTTGGAAGTGGTCCAGACCGCTGTTCTGATAACTGTGGCCCTCCGAGGG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF GX:Z:- GN:Z:- CB:Z:ACAGCAGA_CACTTCGA UB:Z:TTTGTGGGACAG

Thanks!
pdh