Empty input file Reference file does not seem to be a FASTA file

Hello Everyone , i hope you're doing well

i'm using Gap Filler , after scaffolding , in LIbrary file i specefied Bowtie for mapping , but it didn't work i ve got this error message :

ITERATION 1:

=>Sat Apr 18 18:10:40 2020: Mapping reads to scaffolds, reading bowtie output and storing unmapped reads
Warning: Empty input file
Reference file does not seem to be a FASTA file

i don't know what went wrong , my reference File seems to be in Fasta file