I am trying to run bowtie-build in Bowtie2 in order to create the index files for mapping and everytime i am running my script there is a warning
Warning: Encountered reference sequence with only gaps
Furthermore when check the index files i have only *1.bt2 *2.bt2 *3.bt2 *4.bt2 files but not the .rev files and without this its not possible to use bowtie align . Here is my script for bowtie-build :
./bowtie2-build --offrate 1 AGPv4.fa AGPv4
Any way to solve this problem ??