tophat-fusion-post: IndexError: list index out of range

Question

[Emily072020]

Hi,

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()[0])
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.

[lieven.sterck]

I still suspect you have a mix-up between sequences and annotation files?

you will typically get this error when you are requesting a region from a sequence that is not present (eg. you look for 1Mb-1,1Mb and the sequence only has 990Kb length)

in order words: do double check the sequence naming in your fasta and gff(?) file , also make sure you don't have double IDs or things like that.

[Emily072020]

Thanks. The whole procedure was working well before. Only lately, this error starts showing up. I am wondering, if there are problems as you suspect, it should not work from the beginning. Or?

[lieven.sterck]

hard to say, some tools/software is less picky than others .

if it was working before, what then changed now? new input? new tool version?