Crashed with error "'bowtie-build' failed to create breakpoint index"

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What steps will reproduce the problem?
Running chimerascan-0.4.5 with command line arguments with Paired End RNA-Seq 
data

What is the expected output? What do you see instead?
A <filename>.bedpe was expected output.
I see the error "'bowtie-build' failed to create breakpoint index" instead.

What version of the product are you using? On what operating system?
chimerascan-0.4.5, OS is Linux compute000 2.6.32-220.el6.x86_64 #1 SMP Wed Nov 
9 08:03:13 EST 2011 x86_64 x86_64 x86_64 GNU/Linux

Please provide any additional information below.
I am not sure why it failed, because I ran it previously for other sample and 
chimerascan ran for 3-4 days but did give me a result .bedpe file.

Original issue reported on code.google.com by chavan.s...@gmail.com on 9 Apr 2014 at 3:22

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Did you ever receive a response on how to fix this issue? I just ran into it 
and I believe that it is due to an empty breakpoint.fa file being supplied to 
bowtie. I have run multiple other fusion finding programs on this data and 
there are verified fusions present so the breakpoint.fa file should not be 
empty. This is the error message in the log file:
Input files DNA, FASTA:
  /media/sf_E_DRIVE/RNAseq_BAMs/Full_analysis/chimerascan/test2/tmp/breakpoints.fa
Reading reference sizes
Warning: Empty input file
Error: No unambiguous stretches of characters in the input.  Aborting...

Any help on the matter would be greatly appreciated.

Original comment by mgower...@gmail.com on 15 Apr 2015 at 6:36

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I haven't received a response on it. 
Let me know if you are able to find a solution/work around this issue.

Thanks.

Original comment by chavan.s...@gmail.com on 15 Apr 2015 at 7:16

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Same problem here on the tests datasets

Original comment by marc.del...@gmail.com on 17 Jun 2015 at 12:18