TopHat Error: Splice sequence indexing failed with err =255

[EugeneID]

I run tophat-2.0.5.Linux_x86_64 on real and test_ref data and get the same error:

$ tophat -r 20 test_ref reads_1.fq reads_2.fq
[2012-09-24 16:15:37] Beginning TopHat run (v2.0.5)
-----------------------------------------------
[2012-09-24 16:15:37] Checking for Bowtie
Bowtie 2 not found, checking for older version..
Bowtie version: 0.12.7.0
[2012-09-24 16:15:37] Checking for Samtools
Samtools version: 0.1.18.0
[2012-09-24 16:15:37] Checking for Bowtie index files
[2012-09-24 16:15:37] Checking for reference FASTA file
[2012-09-24 16:15:37] Generating SAM header for test_ref
format: fastq
quality scale: phred33 (default)
[2012-09-24 16:15:39] Preparing reads
left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
[2012-09-24 16:15:39] Mapping left_kept_reads to genome test_ref with Bowtie
[2012-09-24 16:15:40] Mapping left_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2012-09-24 16:15:40] Mapping left_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2012-09-24 16:15:40] Mapping left_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2012-09-24 16:15:40] Mapping right_kept_reads to genome test_ref with Bowtie
[2012-09-24 16:15:41] Mapping right_kept_reads_seg1 to genome test_ref with Bowtie (1/3)
[2012-09-24 16:15:41] Mapping right_kept_reads_seg2 to genome test_ref with Bowtie (2/3)
[2012-09-24 16:15:41] Mapping right_kept_reads_seg3 to genome test_ref with Bowtie (3/3)
[2012-09-24 16:15:41] Searching for junctions via segment mapping
[2012-09-24 16:15:42] Retrieving sequences for splices
[2012-09-24 16:15:42] Indexing splices
[FAILED]
Error: Splice sequence indexing failed with err =255

What do I miss?

[EugeneID]

OK. I found that the last version of Bowtie (0.12.8.0) does not show this error.
So it looks like it's a bug in the old version of Bowtie (0.12.7.0).