[Solved] Error reading _ebwt[] array

I was running Tophat2 which calls bowtie2
I got this error:

[2016-05-10 14:51:40] Reading known junctions from GTF file

[2016-05-10 14:51:51] Preparing reads

         left reads: min. length=34, max. length=34, 1745 kept reads (1 discarded)

        right reads: min. length=24, max. length=24, 1746 kept reads (0 discarded)

[2016-05-10 14:51:51] Using pre-built transcriptome data..

[2016-05-10 14:52:06] Mapping left_kept_reads to transcriptome Mus_musculus.NCBIM37.67.filtered with Bowtie2

[2016-05-10 14:52:18] Mapping right_kept_reads to transcriptome Mus_musculus.NCBIM37.67.filtered with Bowtie2

[2016-05-10 14:52:30] Resuming TopHat pipeline with unmapped reads

Warning: you have only one segment per read.

        If the read length is greater than or equal to 45bp,

        we strongly recommend that you decrease --segment-length to about half the read length because TopHat will work better with multiple segments

[2016-05-10 14:52:30] Mapping left_kept_reads.m2g_um to genome mm9-single-cell-NIST-fixed-spikes with Bowtie2

        [FAILED]

Error running bowtie:

Error reading _ebwt[] array: 278873280, 873486272

Error: Encountered internal Bowtie 2 exception (#1)

Command: /woldlab/castor/proj/programs/bowtie2-2.1.0/bowtie2-align --wrapper basic-0 -k 200 -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 4 --sam-no-hd -x /woldlab/castor/proj/genome/bowtie2-indexes/mm9-single-cell-NIST-fixed-spikes -

bowtie2-align exited with value 1

I rebuilt the bowtie2 index in a separate folder and used the newly built index.

It worked!