[Samtools-help] NO_COOR reads not in a single block at the end 0 -1 even though longest chromosome is only +249Mbp

[Stefan N. <ste...@gm...>]

Greetings samtools-list members,

I'm assisting an associate with some calculations, and we've run into some
problems with samtools.
What I'm trying to do is to generate a .bai index file but I get the
following error message:

NO_COOR reads not in a single block at the end 0 -1

I found the suggestion to add -c to samtools which did not help. I also
found at http://sourceforge.net/p/samtools/mailman/message/33155863/ the
suggestion that samtools only supports chromosome length of 512Mbp for
index generation. However our longest chromosome is +248Mbp, far from
512Mbp.

Any help would be appreciated!


Cheers,
/Stefan