Error joing segment hits in tophat

[Wallysb01]

Can anyone offer advice on what to do about this error -11, or even what it means:

[Fri Mar 11 15:54:38 2011] Beginning TopHat run (v1.2.0)
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[Fri Mar 11 15:54:38 2011] Preparing output location tophat_out/cDNA/organ/
[Fri Mar 11 15:54:38 2011] Checking for Bowtie index files
[Fri Mar 11 15:54:38 2011] Checking for reference FASTA file
[Fri Mar 11 15:54:38 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Fri Mar 11 15:54:38 2011] Checking for Samtools
Samtools Version: 0.1.12a
[Fri Mar 11 15:54:40 2011] Checking reads
min read length: 21bp, max read length: 991bp
format: fasta
[Fri Mar 11 15:54:41 2011] Mapping reads against Anocarol2.0.61_toplevel with Bowtie
[Fri Mar 11 15:55:05 2011] Joining segment hits
[FAILED]
Error: Segment join failed with err = -11

[emreis]

We are experiencing exactly the same error mentioned in the post above running a particular batch of 454 RNAseq. The same version of TopHat (v1.2.0) was used.
I could not find a list with details of TopHat error codes. That would be useful for troubleshooting.