Getting An Error When Running Tophat-Fusion-Post

Question

[Andrew]

I ran tophat with the following command:

tophat-2.0.3.Linux_x86_64/tophat2 \
  -o ./tophat_pig \
  -p 8 \
  --fusion-search \
  --keep-fasta-order \
  --bowtie1 \
  --no-coverage-search \
  -r 50 \
  --mate-std-dev 80 \
  --fusion-min-dist 100000 \
  --fusion-anchor-length 13 \
  --fusion-ignore-chromosomes chrM \
  /WPS/RNA/liangpeiquan/data/bowtie-0.12.8/indexes/Sus_scrofa \
  Sus_scrofa_1.fq Sus_scrofa_2.fq

And I got the usual result files.

Then, I want to run tophat-fusion-post,so I set my folders like this:

refgene.txt
ensgene.txt
mcl
tophat_pig
blast

and my tophat-fusion-post script.

/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post \
  -p 8 \
  --num-fusion-reads 1 \
  --num-fusion-pairs 2 \
  --num-fusion-both 5 \
  /WPS/RNA/liangpeiquan/data/bowtie-0.12.8/indexes/Sus_scrofa

then I ran the shell script,but I got the command like this:

[Wed Nov 21 10:27:09 2012] Beginning TopHat-Fusion post-processing run (v2.0.6)
[Wed Nov 21 10:27:10 2012] Extracting 23-mer around fusions and mapping them using Bowtie
[Wed Nov 21 10:31:45 2012] Filtering fusions
    Processing: tophat_pig/fusions.out

Traceback (most recent call last):
File "/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post", line 2091, in <module>
sys.exit(main())

File "/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post", line 2062, in main
filter_fusion(bwt_idx_prefix, params)

File "/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post", line 700, in filter_fusion
filter_fusion_impl(fusion_file, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list)

File "/WPS/RNA/liangpeiquan/software/tophat-2.0.6.Linux_x86_64/tophat-fusion-post", line 426, in filter_fusion_impl
kmer_len = len(seq_chr_dic.keys()[0])

IndexError: list index out of range

Can anybody give me a hand to solve this problem?

Thank you very much!

[Paul]

Hello all,

Please can you tell me where I will get mcl file? I am not able to find it.

Thank you for any help,

Paul

Answer 1

[mknut]

This question has been answered here: Tophat-Fusion-Post Error To sum up - put both bowtie 1 and bowtie 2 indexes in your index folder (/WPS/RNA/liangpeiquan/data/bowtie-0.12.8/indexes/ in your case). It worked for me and it seems to be working for others.