Strange TopHat (.11 and .12) 'out_of_range' Error

[muppetjones]

Here is the error:

[2014-11-06 09:50:48] Building transcriptome data files <<genome>>
	[FAILED]
 Error: gtf_to_fasta returned an error.

Which leads to the g2f.err file:

terminate called after throwing an instance of 'std::out_of_range'
  what():  basic_string::substr

This problem is usually caused by issues with the annotation file, but:

[07.11 11:01:21 5] $ gt gff3validator ~/sshfs/bronco/genomes/hs_ref_GRCh37.p13.gff 
input is valid GFF3

or due to a mismatch between names, but:

** truncated due to size **
[07.11 11:00:53 3] $ bowtie2-inspect -n hs_ref_GRCh37.p13
chr1
chr10
chr11
chr12
...
[07.11 11:07:44 6] $ cut -f1 hs_ref_GRCh37.p13.gff | sort | uniq
... [NW_*, NT_*] ...
chr1
chr10
chr11
chr12
...

Background

I was using TopHat 2.0.11 on a server with a local (my HOME) BowTie 2.2.1 install due to the documented incompatibility with 2.0.11 and newer versions of BowTie. This worked just fine. Then, the server admin updated to TopHat 2.0.12 (the only known change...), and everything crumbles.

I have tried using local TopHat 2.0.11 binaries, loading 2.0.11 through Modules (which may or may not be set up properly), and using the 2.0.12 (and everything else) installed on the server. Nothing fixes the problem.

If it only crashed with some genomes, that would be one thing, but now it's not working with any genome, even those that previously ran fine. I'm at a complete loss at how to solve the problem, and any help would be greatly appreciated.

Summary:
Genomes (all worked previously, except GRCh37.p13, which wasn't tested):
* RheMac (latest from NCBI)
* Human (GRCh37.p5 and GRCh37.p13)
* Tuberculosis (h37r[av] from tbdb.org)
Worked:
* tophat 2.0.11 (server) w/ bowtie 2.2.1 (local, i.e., ~/local)
Did not work:
* tophat 2.0.12 (server) w/ bowtie 2.2.1 (local)
* tophat 2.0.12 (server) w/ bowtie 2.2.3 (server) -- removed my .bashrc
* tophat 2.0.11 (local binaries) w/ bowtie 2.2.1 (local)
* tophat 2.0.11 (server module) w/ bowtie 2.2.1 (local) and 2.2.3 (server)

Thanks!