Question: samtools " Assertion `iter->curr_off == iter->off[iter->i].v' failed". "
0
gravatar for liushang
8 months ago by
liushang0
liushang0 wrote:

Hi, I meet a problem when I run samtools. The error message is

 "bam_index.c:695: bam_iter_read: Assertion `iter->curr_off == iter->off[iter->i].v' failed".

I would like to ask how the question happened and how to resolve it. Thank you !

samtools • 189 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by liushang0

is your bam sorted ? is your bai file up-to-date ?

ADD REPLYlink written 8 months ago by Pierre Lindenbaum123k

Please provide the exact command your were using.

Also what version of samtools do you have?

ADD REPLYlink written 8 months ago by finswimmer12k
1
gravatar for John Marshall
8 months ago by
John Marshall1.7k
Glasgow, Scotland
John Marshall1.7k wrote:

That error message indicates that you are using samtools 0.1.19. This was released almost six years ago, and still using it is a problem in itself…

ADD COMMENTlink written 8 months ago by John Marshall1.7k
0
gravatar for liushang
8 months ago by
liushang0
liushang0 wrote:

Thank you very much ! The problem has been solved. I edit the bam header and then the command can run.

ADD COMMENTlink written 8 months ago by liushang0
1

Could you please provide more information about what was the problem with your header and how you have fixed it.

Doing this, you can help other people facing the same problem to solve it.

Thanks!

fin swimmer

ADD REPLYlink written 8 months ago by finswimmer12k
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