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

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?

Cheers,

Lionel


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