Getting an error when running tophat-fusion-post

Posted 2023-04-28

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 commond 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?
Thankyou very much!

参考技术A 我也遇到过这个问题，可能是gtf文件和refGene.txt ensGene.txt 内容不匹配 参考技术B 想请教一下做小鼠的tophatfusion应该怎么做？

TMS Error when opening an RFC connection

2173569 - Error when opening an RFC connection

问题:

 

 

 

 

Environment

• SAP Release Independent.

Reproducing the Issue

• Execute a transport tools check;
• Refresh the transport queue.

Cause

• Problem with tp;
• Parameter rfc/use_gwstart not set to 1.

Resolution

• Make sure tp is updated to the latest version available in the service marketplace;
• Set parameter rfc/use_gwstart = 1 in the profile and restart the instance.