[mira_talk] FW: Ssaha-Mira question

Hi Bastien

Having used the suggestions you made below as to parameterizing ssaha2 to 
identify contaminating cloning adapters, I then launched mira (2.0.0) thusly:

nohup mira --project=CRW_GEP_454_Body_10302009 --job=denovo,est,normal,454 
COMMON_SETTINGS -GE:not=4 
-FN:xtii='sample1_traceinfo_in.454.xml':svsi='sample1.fasta_vs_clonetech_adpaters.fasta.ssaha2'
 454_SETTINGS -LR:mxti=yes -CL:msvs=yes >& log_assembly3.txt &

$ tail log_assembly3.txt

Merging data from XML trace info file sample1_traceinfo_in.454.xml ...Num 
reads: 1091861
Building hash table ... done.
Localtime: Mon Jan  4 08:59:59 2010

Generated 1091861 unique template ids for 1091861 valid reads.
Done merging XML data, matched 1091861 reads.


Starting clips:  done.
Localtime: Mon Jan  4 09:00:07 2010

Merging vector screen data from SSAHA results file 
sample1.fasta_vs_clonetech_adpaters.fasta.ssaha2
...Building hash table ... done.


Here it has remained for several hours

-bash-3.1$ top
  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
 3660 rosema1   25   0 1958m 1.9g 1352 R  101  2.2 348:50.91 mira

-bash-3.1$ strace -p 3660
-bash-3.1$ strace -p 3660
Process 3660 attached - interrupt to quit
<after many minutes of no activity I quit>
Process 3660 detached
-bash-3.1$


Is something wrong here?  I found a similar post in mira_talk but saw no 
followup to resolve it

Thanks for your help.

Mark


-----Original Message-----
From: Bastien Chevreux [mailto:bach@xxxxxxxxxxxx] 
Sent: Sunday, January 03, 2010 6:59 PM
To: Rose Mark USRE
Subject: Re: Ssaha-Mira question

On Montag 04 Januar 2010 mark.rose@xxxxxxxxxxxx wrote:
> I noticed your MIRA update that permits use of ssaha2 output to mask
>  sequence for a mira assembly.  Thanks. Would you mind being a little more
>  explicit about any parameterization of ssaha2 required by MIRA (i.e.
>  output format, etc.)? Thanks Again

Does this help?

Note 1: the output format of SSAHA2 must the native output format (-output 
ssaha2). Other formats cannot be parsed by mira. 
 Note 2: I currently use the following SSAHA2 options: -kmer 8 -skip 1 -seeds 
1 -score 12 -cmatch 9 -ckmer 6 
 Note 3: the sequence vector clippings generated from SSAHA2 data do not 
replace sequence vector clippings loaded via the EXP, CAF or XML files, they 
rather extend them.

From the main documentation file. There's also a very short example in 
mira_usage.

Regards,
  Bastien

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