samtools-help

[Samtools-help] tabix error "the chromosome blocks not continuous"

[Ogan <ab...@gm...>]

Dear all,

I have a refgene file that I tabix for fast access. I am getting 
"[ti_index_core] the chromosome blocks not continuous at line 75, is the 
file sorted? [pos 1]" error with tabix version 0.2.5 (r1005). What is 
strange is the same file works fine on 0.2.5 (r964). When I inspect the 
file the only problem is that there are multiple entries at the same 
position (file is sorted by the way). So the the positional numbers are 
not consecutive but they are same (sometimes). So when I want to search 
the file, I would like to retrieve multiple lines for the same position. 
It has been a while since I have used tabix and all the files I 
generated worked fine until recently, but not with the newer tabix 
version. I thought you could have the same key multiple times in the 
file. Does anybody have any idea?

Best,

Ogan

Re: [Samtools-help] tabix error "the chromosome blocks not continuous"

[Petr D. <pd...@sa...>]

Hi Ogan,

is it possible that the column indexes in the file do no correspond
those supplied on command line (-s,-b,-e)? Best if you could provide a
small example to reproduce the problem. 

Petr


On Wed, 2013-08-28 at 15:54 -0400, Ogan wrote:
> Dear all,
> 
> I have a refgene file that I tabix for fast access. I am getting 
> "[ti_index_core] the chromosome blocks not continuous at line 75, is the 
> file sorted? [pos 1]" error with tabix version 0.2.5 (r1005). What is 
> strange is the same file works fine on 0.2.5 (r964). When I inspect the 
> file the only problem is that there are multiple entries at the same 
> position (file is sorted by the way). So the the positional numbers are 
> not consecutive but they are same (sometimes). So when I want to search 
> the file, I would like to retrieve multiple lines for the same position. 
> It has been a while since I have used tabix and all the files I 
> generated worked fine until recently, but not with the newer tabix 
> version. I thought you could have the same key multiple times in the 
> file. Does anybody have any idea?
> 
> Best,
> 
> Ogan
> 




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