[mira_talk] Re: Assembly fails with flag -CL:msvs=yes

Hi Lionel,

2009/5/26 Lionel Guy <guy.lionel@xxxxxxxxx>

> Hi there,
>
> I've tried to run a reference assembly with mira, and it failed, saying
> that there was 1 megahub in my sequence. I thought I had carefully
> clipped the sequence (using lucy with -vector enabled), but was not too
> sure... so I tried to enable the -CL:msvs falg in mira, but it failed to
> find some file. I'm not sure if I should have ssaha present in my path,
> should I? In that case, which version? I have ssaha2 installed.
>
> The complete command was:
>
> mira --project=BHUGA10NrSrM01 -fasta
> --job=mapping,genome,sanger,454,accurate -OUT:ora=yes -GE:not=3
> -AS:urd=yes -SB:lb=yes:bft=fasta:bbq=40:abnc=yes -CL:msvs=yes >
> assembly_log.txt
>
>
> At one point, mira starts to work with ssaha results:
>
> Merging vector screen data from SSAHA results file
> BHUGA10NrSrM01_ssahavectorscreen_in.txt ...Building hash table ... done.
>
> But then later:
>
> Fatal Error: "BHUGA10NrSrM01_ssahavectorscreen_in.txt"
> : File not found.
> ->Thrown: void Assembly::mergeSSAHAVecScreenData(const string &
> ssahafile)
> ->Caught: main
> Program aborted.
>
>
> Any suggestion?
>

You need to generate the BHUGA10NrSrM01_ssahavectorscreen_in.txt file before
you run mira, e.g.

$ ssaha BHUGA10NrSrM01.fasta Vector.seq -da 0 -pf -qf fasta -sf fasta  >
BHUGA10NrSrM01_ssahavectorscreen_in.txt

hth,
Sven



>
> Cheers,
>
> Lionel
>
>
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