while runnning tophat-fusion-post, I got errors:
[Tue Jul 7 13:24:20 2020] Filtering fusions Processing: tophat_test/fusions.out Traceback (most recent call last): File "/usr/tophat-2.0.9/tophat-fusion-post", line 2646, in <module> sys.exit(main()) File "/usr/tophat-2.0.9/tophat-fusion-post", line 2617, in main filter_fusion(bwt_idx_prefix, params) File "/usr/tophat-2.0.9/tophat-fusion-post", line 707, in filter_fusion filter_fusion_impl(fusion_file, refGene_list, ensGene_list, seq_chr_dic, fusion_gene_list) File "/usr/tophat-2.0.9/tophat-fusion-post", line 428, in filter_fusion_impl kmer_len = len(seq_chr_dic.keys()) IndexError: list index out of range
I have tried:
(1) delete the folder "tophatfusion_out" and run another time. ==> same error
(2) put both of Bowtie 1 and 2 index at the correct location as suggested: http://seqanswers.com/forums/showthread.php?t=21267 and Tophat-Fusion-Post Error
My bowtie 1 index should be fine, because the previous step has successfully generated "fusions.out".
(3) I've tried tophat 2.1.0 and tophat 2.1.1, which give the same errors.
(4) Some people have this error because one file has "chr", yet another one file has only numbers. In my case, my files all have "chr".
All I have tried above still give me the same error.
Any one has another idea? Thanks a lot.