Off topic:Tophat-Fusion-Post Error

Question

[Richard]

I ran tophat2 with the following command:

tophat-2.0.3.Linux_x86_64/tophat -p 6 --fusion-search -o outDir/ hg19 hg19.r1.fq hg19.r2.fq

I got all the usual tophat output files, including the fusions.out file. Next I want to run tophat-fusion-post.

I set up my folders as directed:

ls $
blast_human
ensGene.txt
mcl
refGene.txt
tophat_sim01
tophat_sim03

When I try and run my command I get a criptic error:

tophat-2.0.3.Linux_x86_64/tophat-fusion-post --output-dir tophatfusion_out ../tophat_fusion_refs/hg19
[Tue Jun 19 14:36:11 2012] Beginning TopHat-Fusion post-processing run (v2.0.3)
-----------------------------------------------
[Tue Jun 19 14:36:11 2012] Extracting 23-mer around fusions and mapping them using Bowtie
[Tue Jun 19 14:36:11 2012] Filtering fusions
        Processing: tophat_sim01/fusions.out
Traceback (most recent call last):
  File "/home/rcorbett/aligners/tophat2/tophat-2.0.3.Linux_x86_64/tophat-fusion-post", line 2083, in ?
    sys.exit(main())
  File "/home/rcorbett/aligners/tophat2/tophat-2.0.3.Linux_x86_64/tophat-fusion-post", line 2054, in main
    filter_fusion(bwt_idx_prefix, params)
  File "/home/rcorbett/aligners/tophat2/tophat-2.0.3.Linux_x86_64/tophat-fusion-post", line 695, in filter_fusion
    filter_fusion_impl(fusion_file, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list)
  File "/home/rcorbett/aligners/tophat2/tophat-2.0.3.Linux_x86_64/tophat-fusion-post", line 422, in filter_fusion_impl
    kmer_len = len(seq_chr_dic.keys()[0])
IndexError: list index out of range

In the output folder I have

ls $
fusion_seq.bwtout
fusion_seq.fa
fusion_seq.map
sample_list.txt

but only the sample_list.txt and fusion_seq.fa are non-empty files. Can anyone provide with with some help?