Tophat2 can't find Bowtie index files *.ebwt

[huan]

I have run tophat2 using cmd:
tophat2 --bowtie1 -p 6 -G /project/Ref_Genome/GRCm38.gtf -N 2 -r 40 --library-type fr-unstranded -o ./ /project/Ref_Genome/GRCm38.genome.fa /project/rawdata/mouse-1.fq /project/rawdata/mouse-2.fq
but the following error occurs:
Error: Could not find Bowtie index files /project/Ref_Genome/GRCm38.genome.fa.*.ebwt)
I have checked that /project/Ref_Genome/GRCm38.genome.fa.*.ebwtl is produced.

My software infomation is here:
bowtie version 1.1.1
TopHat v2.0.13

Any suggestion?
Thanks a lot!

[dpryan]

This might be fixed in a more recent version. Not all of the versions have properly supported large indices for both bowtie1 and bowtie2.

[huan]

Thanks a lot @dpryan!
I will have a try using bowtie2.