other problems with tophat 1.1.3

[zorph]

I tried running my SOLiD reads on Tophat 1.1.3 after they exited due to a bug from 1.1.2 last night only to get the following error message:

[Tue Nov 16 16:58:40 2010] Beginning TopHat run (v1.1.3)
-----------------------------------------------
[Tue Nov 16 16:58:40 2010] Preparing output location /r/solid_xfer/Internal/AD/M_KOHLI/AD6/Analysis/TopHat_8//
[Tue Nov 16 16:58:40 2010] Checking for Bowtie index files
[Tue Nov 16 16:58:40 2010] Checking for reference FASTA file
[Tue Nov 16 16:58:40 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Nov 16 16:58:40 2010] Checking for Samtools
Samtools version: 0.1.8.0
[Tue Nov 16 17:03:01 2010] Checking reads
min read length: 50bp, max read length: 50bp
format: fasta

here was my input:
/tophat -C --quals -o /r/TopHat_8 --library-type fr-secondstrand -p 8 /hg18_c_index/hg18_c /r/reads.csfasta /r/reads.qual


Can anyone tell me what could possibly be wrong. I ran the same line on v1.1.2 and it ran until the bug in the program made it stop.

Thanks in advance.

Zorph