[mira_talk] Fwd: Assembly with clean sequences

Re-posted as the original mail did not get through.

> From ...  Tue Mar 24 16:30:11 2009
> Hi,
> May be I did not read the manual thoroughly. I am trying to run a bunch of
> trace sequences pre-cleaned of vectors, low quality. My fasta file contains
> just good quality sequences and I tried to run mira with the following
> options:
> ./bin/mira -fasta=./sequences/HpMira_in.sanger.fasta 
> -job=sanger,denovo,normal,genome -LR:mxti=no
>
> and it exits with the following error. 
> Short length: HPAA-acn43c10.b1 (san): only 0 good bases, need: 80. No paired 
> end partner, rejected.
> Short length: HPAA-acn43c11.b1 (san): only 0 good bases, need: 80. No paired
> end partner, rejected.
> Short length: HPAA-acn43c12.b1 (san): only 0 good bases, need: 80. No paired
> end partner, rejected.
> ./runMira.sh: line 1: 14648 Floating point exception./bin/mira 
> -fasta=./sequences/HpMira_in.sanger.fasta -job=sanger,denovo,normal,genome 
> -LR:mxti=no
>
> Is there an easy way to run just clean sequences without providing any
> quality files?

Hi Sucheta,

yes, there is. Switch off the clips that are based on quality values. These 
would be:
   -CL:qc=no:bsqc=no

As MIRA also has per default clips turned on that ensure minimum clips when no 
ancillary data is loaded, the minimum clips also need to be turned off: 
  -CL:emlc=no:emrc=no

For the lazy: using "-noclipping" turns off each and every clip for every 
sequencing technology. Note that "-noclipping" is an order dependend quick 
switch: place it *after* --job=... or else --job=... will overwrite the -
noclipping effect.

Regards,
  Bastien


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