Hi

I was install bowtie2 (apt-get install bowtie, bowtie2, samtools)

and version is

/usr/bin/bowtie2-align version 2.1.0

I ran tophat2 for RNA-seq mapping, but this error message popped up.

[2015-12-10 14:56:25] Beginning TopHat run (v2.0.9)

-----------------------------------------------
[2015-12-10 14:56:25] Checking for Bowtie
          Bowtie version:     2.1.0.0
[2015-12-10 14:56:25] Checking for Samtools
        Samtools version:     0.1.19.0
[2015-12-10 14:56:26] Checking for Bowtie index files (transcriptome)..
[2015-12-10 14:56:26] Checking for Bowtie index files (genome)..
[2015-12-10 14:56:26] Checking for reference FASTA file
[2015-12-10 14:56:26] Generating SAM header for /home/genome/Homo_sapiens/hg19
    format:         fastq
    quality scale:     phred33 (default)
[2015-12-10 14:56:36] Reading known junctions from GTF file
[2015-12-10 14:56:38] Preparing reads
     left reads: min. length=20, max. length=101, 17432242 kept reads (15275 discarded)
    right reads: min. length=20, max. length=101, 17439959 kept reads (7558 discarded)
[2015-12-10 15:07:27] Using pre-built transcriptome data..
[2015-12-10 15:07:32] Mapping left_kept_reads to transcriptome hg19_transcripts with Bowtie2
    [FAILED]
Error running bowtie:
Error reading _ebwt[] array: 50459520, 50652672
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/bin/bowtie2-align -q -k 60 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2 --np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 1 --sam-no-hd -x /home/genome/Homo_sapiens/hg19_transcripts -

My command is

tophat2 -o output -G  GTFfile --transcriptome-index /home/genome/Homo_sapiens/hg19_transcripts --library-type fr-firststrand /home/genome/Homo_sapiens/hg19 sample1.fastq sample2.fastq

Before running tophat, bowtie2-build also I did.

How can I solve this Error?