Re: [wgs-assembler-users] Make-consensus errors in pacBioToCA

[Sergey K. <se...@um...>]

Hi,

That certainly doesn't look normal, especially the over 100% error rates. Could you post one of your asm.*.lay and asm.*.log files. Either one that failed or one that had over 100% error.

Sergey

On Apr 23, 2013, at 1:32 PM, Ole Kristian Tørresen <o.k...@ib...> wrote:

> Hi,
> I'm correcting some XLXL PacBio reads, and hit upon some failed assertions in make-consensus. I hope it's possible to solve.
> 
> This is the first error (last 10 lines of the out file from the runPartition.sh):
>   with 100 errors (99.01% error)
> In contig 814 forced alignment of 65 bases of string 48036185 subscript 344 to 2 bases of consensus
>   with 64 errors (98.46% error)
> In contig 814 forced alignment of 398 bases of string 52752554 subscript 345 to 1 bases of consensus
>   with 397 errors (99.75% error)
> In contig 814 forced alignment of 227 bases of string 56213438 subscript 346 to 18 bases of consensus
>   with 214 errors (94.27% error)
> In contig 814 forced alignment of 112 bases of string 75693310 subscript 347 to 2 bases of consensus
>   with 110 errors (98.21% error)
> make-consensus: align.cc:4903: void Complete_Align(const char*, int, int, const char*, int, int, int, int, int, int, int, Align_Score_Entry_t*, Align_Score_Entry_t&, Alignment_t&): Assertion `t_lo < t_slip' failed.
> 
> 98.21 % error is a bit weird. Got any idea what that assertion is?
> 
> 
> This is not an error, but even weirder:
>   with 62 errors (151.22% error)
> In  Reset_From_Votes  in contig 1369
>   Forced alignment of string subscript 685 to consensus
>   with 169 errors (174.23% error)
> In  Reset_From_Votes  in contig 1369
>   Forced alignment of string subscript 686 to consensus
>   with 154 errors (179.07% error)
> In  Reset_From_Votes  in contig 1369
>   Forced alignment of string subscript 687 to consensus
>   with 78 errors (185.71% error)
> 
> 185.71 % error? That's a lot.
> 
> This is another error:
> In contig 1135 forced alignment of 82 bases of string 52574042 subscript 809 to 11 bases of consensus
>   with 74 errors (90.24% error)
> In contig 1135 forced alignment of 225 bases of string 41625223 subscript 810 to 3 bases of consensus
>   with 222 errors (98.67% error)
> In contig 1135 forced alignment of 146 bases of string 55029895 subscript 811 to 2 bases of consensus
>   with 144 errors (98.63% error)
> In contig 1135 forced alignment of 140 bases of string 40943538 subscript 812 to 3 bases of consensus
>   with 137 errors (97.86% error)
> ERROR:  Bad from = 3 in Global_Align
>   in file  align.cc  at line  6872  errno = 0
> 
> How can I get this kind of errors in the alignments? 
> 
> The genome is about 830 Mbp (it's cod). Correcting with 454 reads, about 27x total. This is about 3.5x coverage in PacBio reads:
> Running with 2536048074 bp for pblr_XLXL_cod.
> Correcting with 22252248087 bp.
> 
> Could something have gone wrong in the correctPacBio step? 
> 
> Thank you.
> 
> Ole
> 
> 
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