Tophat Fusion Post error

[pbpayal]

Hi,
I want to annotate tophat fusions.out file with gene names. So after running Tophat with --fusion-search option, I got fusions.out file. Now I want to run tophat-fusion-post. I have cretaed the recommneded diretory structure and have installed blast database and have installed blast by blast.dmg for my mac according to blast website.

When I run the following, I am getting error:
tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 indexes/hg38

I have directory structure:
Tophat_DIr
--blast
--indexes
--tophatoutputsample

•              --accepted_hits.bam
  

•              --align_summary.txt
  

•              --deletions.bed
  

•              --fusions.out
  

•              --insertions.out
  

•              --junctions.bed
  

•              --logs
  

•              --prep_reads.info
  

•              --unmapped.bam
  

--ensGene.txt
--refGene.txt

Error:
Beginning TopHat-Fusion post-processing run (v2.1.0)

[Mon Feb 26 14:32:42 2018] Extracting 23-mer around fusions and mapping them using Bowtie
[Mon Feb 26 14:32:46 2018] Filtering fusions
Traceback (most recent call last):
File "/usr/local/bin/tophat-fusion-post", line 2924, in
sys.exit(main())
File "/usr/local/bin/tophat-fusion-post", line 2895, in main
filter_fusion(bwt_idx_prefix, params)
File "/usr/local/bin/tophat-fusion-post", line 965, in filter_fusion
ensGene_list = read_genes("ensGene.txt")
File "/usr/local/bin/tophat-fusion-post", line 917, in read_genes
num_exons = int(line[7])
ValueError: invalid literal for int() with base 10: 'exonCount'

Can anyone please tell me whats going wrong?

Thanks,
Payal

[matq007]

Have you tried this #45? Removed the error for me, but I'm not getting any fusions. I think it's a parameter issue for me.