Tophat-fusion-post error

[dadada4ever]

Hi everyone, I have a question when using tophat-fusion-post, and any suggestions would be greatly appreciated.

I use the tophatfusion-0.1.0 (the old version) to do the tophat-fusion and the results seems fine. But when I use the tophat-fusion-post:

python /share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5  /share_bio/panfs/zengchq/baij/HumanRef/BowtieIndex_hs37.67

The error shows:

[Fri Jun 29 16:15:22 2012] Beginning TopHat-Fusion post-processing run (v0.1.0 (Beta))
-----------------------------------------------
[Fri Jun 29 16:15:22 2012] Extracting 23-mer around fusions and mapping them using Bowtie
[Fri Jun 29 16:15:22 2012] Filtering fusions
	Processing: tophat_N/fusions.out
Traceback (most recent call last):
  File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py", line 1904, in <module>
    sys.exit(main())
  File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py", line 1875, in main
    filter_fusion(params)
  File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py", line 632, in filter_fusion
    filter_fusion_impl(fusion_file, refGene_list, ensGene_list, ensGtp_dic, seq_chr_dic, fusion_gene_list)
  File "/share/disk2-4/zengchq/gongkn/tophatfusion-0.1.0/src/tophat-fusion-post.py", line 351, in filter_fusion_impl
    kmer_len = len(seq_chr_dic.keys()[0])
IndexError: list index out of range

The one who occur the same error said it's the reason of Bowtie index and then I tried the Bowtie1 Bowtie2 index separately and even tried to use tophat2 to run my tophat-fusion-0.1.0 results but the errors are all the same. (link here: http://www.biostars.org/post/show/47...ion-post-error).
And my directory structure is:

(top_dir)
Tophat-N
Tophat-T
tophatfusion_out - the output directory by tophat-fusion-post
ensGene.txt 
ensGtp.txt
refGene_sorted.txt
mcl
blast_human - blast database

I don't know where the question is, please give me some suggestions...
Thank you,
Conan.

[bioinfo0421]

....................

[lpqsx2005]

I have the exactly same error.Have you solved it yet? Can anybody help me?

[dadada4ever]

I have the exactly same error.Have you solved it yet? Can anybody help me?

Nope. IMO you could write perl script to filter out the raw results generated from tophat fusion and acquire the gene name manually.
If your data is sequenced by illumina you could try some other software such as deFuse.

[mknut]

I got identical error and managed to solve it. As advised by Richard on Biostars http://www.biostars.org/p/47369/
What you need to do is place both bowtie 1 and bowtie 2 indexes in one folder (either index them yourself or download from ftp://ftp.cbcb.umd.edu/pub/data/), point tophat-fusion-post to this folder and it should be running. Worked for me.

Command I used:

tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /scratch/EXOME_DATA/RNASEQ/index_combined/hg19

Using:
Tophat 2.0.6
Bowtie 0.12.8
Bowtie2 2.0.2

[lpqsx2005]

I got identical error and managed to solve it. As advised by Richard on Biostars http://www.biostars.org/p/47369/
What you need to do is place both bowtie 1 and bowtie 2 indexes in one folder (either index them yourself or download from ftp://ftp.cbcb.umd.edu/pub/data/), point tophat-fusion-post to this folder and it should be running. Worked for me.

Command I used:

tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /scratch/EXOME_DATA/RNASEQ/index_combined/hg19

Using:
Tophat 2.0.6
Bowtie 0.12.8
Bowtie2 2.0.2

I will have a try.Thank you very much!

[lpqsx2005]

I got identical error and managed to solve it. As advised by Richard on Biostars http://www.biostars.org/p/47369/
What you need to do is place both bowtie 1 and bowtie 2 indexes in one folder (either index them yourself or download from ftp://ftp.cbcb.umd.edu/pub/data/), point tophat-fusion-post to this folder and it should be running. Worked for me.

Command I used:

tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 /scratch/EXOME_DATA/RNASEQ/index_combined/hg19

Using:
Tophat 2.0.6
Bowtie 0.12.8
Bowtie2 2.0.2

It worked！Thank you!

[dadada4ever]

Bump.
I tried to put bowtie1 and bowtie2 indexes together, but program still reported same error.

ConanMacBook-Air:Tophat_fusion Conan$ tophat-fusion-post ../Ref_official_website_ver/hg19_mix/
[Sun Feb 17 17:24:43 2013] Beginning TopHat-Fusion post-processing run (v2.0.7)
-----------------------------------------------
[Sun Feb 17 17:24:44 2013] Extracting 23-mer around fusions and mapping them using Bowtie
[Sun Feb 17 17:24:44 2013] Filtering fusions
Processing: tophat_S4-a/fusions.out
Traceback (most recent call last):
File "/Users/Conan/WorkApps/tophat-2.0.7.OSX_x86_64/tophat-fusion-post", line 2615, in <module>
sys.exit(main())
File "/Users/Conan/WorkApps/tophat-2.0.7.OSX_x86_64/tophat-fusion-post", line 2586, in main
filter_fusion(bwt_idx_prefix, params)
File "/Users/Conan/WorkApps/tophat-2.0.7.OSX_x86_64/tophat-fusion-post", line 704, in filter_fusion
filter_fusion_impl(fusion_file, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list)
File "/Users/Conan/WorkApps/tophat-2.0.7.OSX_x86_64/tophat-fusion-post", line 428, in filter_fusion_impl
kmer_len = len(seq_chr_dic.keys()[0])
IndexError: list index out of range

Can anybody tell me where the standard error file is so that I could find out my specific problem. Since Richard on Biostar said:

When looked in the stderr I found that tophat-fusion-post wanted to use the bowtie1 index for my genome, while I only had the bowtie 2 index, which I used to run tophat 2.

Thank you!

[Nobuyuki Fujii]

I also encountered the same problem and the problem did not resolve the problem immediately after the correction about bowtie index.

Problem was solved after I remove the tophatfusion_out directory that was created by my previous run with error.

Please try it.

Bump.
I tried to put bowtie1 and bowtie2 indexes together, but program still reported same error.


Can anybody tell me where the standard error file is so that I could find out my specific problem. Since Richard on Biostar said:


Thank you!

[jp.]

Hi
I got the trouble with tophatfusio-post.
can you guess something...I posted here:

http://seqanswers.com/forums/showthread.php?p=112615#post112615