[mira_talk] Re: Fwd: ace file output from MIRA

Dear Bastien/all, 

we are also using consed to view MIRA outputs, and it is working fine in 
principle, although there have been a number of small errors. We are still not 
quite sure on why they happen. It also seems to be somewhat unpredictable; for 
some assemblies we get errors and for others not, and we can not quite tell yet 
what the differences are. We are happy to try to help working a bit on this to 
see if we can improve things, and we will let you know how we progress; the 
basic problem is that the consed support is not always great, and we've found 
it hard to find proper definitions of the file formats. 


Now to the question:
Consed is designed to take an .ace file as input, but it also expects that 
there is a .phd-file for each read. (It is also possible to concatenate all 
.phd files into a single file 'phd.ball'.) 

The basic problem is that MIRA does not create the .phd files. To circumenvent 
this problem, you might try to change your run command to  
consed -nophd -ace ./pdt_results/pdt_out.ace
The downside of not having any .phd files is that the quality values for each 
read are only stored in the .phd-files, and so these can not be viewed in 
consed. The quality values of the contigs are ok though. 

We have been thinking of creating .phd files (or rather a phd.ball) directly 
from the MIRA input files, but there might be trouble with some of the clipping 
options, so maybe a wish would be for MIRA to output a full consed folder 
similar to what Newbler does?


Good luck, and hoping to continue this discussion to the benfit of all :)
Björn Nystedt




On Sun, 10 May 2009 10:48:34 +0200
Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

> Dear all,
> 
> I got a question regarding ACE / consed I cannot answer (I don't have 
> consed). 
> I'd be happy if anyone knows what to do (be it on my side or on the user 
> side).
> 
> Regards,
>   Bastien
> 
> Forwarded message
> 
> -----------------------------------------------------------------------------
> 
> [...]
> 
> I think I've got this to run, but I'm running  
> into a problem in examining the output. I can see from the html file  
> that the assembly looks pretty good, but that file is too big to  
> completely load into a browser such as Firefox or Safari.
> 
> I've been trying to use the ace file that was written out by consed  
> but I'm having difficulties. Consed doesn't seem to want to read the  
> file and I'm not sure why this is, but it seems to relate to a problem  
> with the ace file format that is written by MIRA.
> 
> The error message I get is:
> 
> [biocperformance:pdt/chromat_all/pdt_assembly2] craigm% consed -ace ./ 
> pdt_results/pdt_out.ace
> Darwin Version: 9.6.0
> no ~/.consedrc file so no user resources will be used--that's ok
> no ./.consedrc file so no project-specific resources--that's ok
> couldn't open readOrder.txt--that's ok
> exception thrown: ace file error detected from source file  
> parseAceFile.cpp at 2495
> Error in file ./pdt_results/pdt_out.ace at line 212.  Line:
> DS SCF_FILE: B24PDT_35_096.bab1.scf
> 
> "neither VERSION: nor PHD_FILE: not found" on this DS line.  This may  
> be missing because you didn't use phredPhrap and phd2fasta (which is  
> called by phredPhrap).  These programs were downloaded with consed so  
> you have them
> 
> ace file: ./pdt_results/pdt_out.ace
> Version 19.0 (090206)
> ace file error detected from source file parseAceFile.cpp at 2495
> Error in file ./pdt_results/pdt_out.ace at line 212.  Line:
> DS SCF_FILE: B24PDT_35_096.bab1.scf
> 
> "neither VERSION: nor PHD_FILE: not found" on this DS line.  This may  
> be missing because you didn't use phredPhrap and phd2fasta (which is  
> called by phredPhrap).  These programs were downloaded with consed so  
> you have them
> ace file = ./pdt_results/pdt_out.ace
> Version 19.0 (090206)
> 
> It may also be that consed is expecting to find other files, but I'm  
> having trouble working out if this is the problem.
> 
> I've also tried other programs that should be able to read ace files  
> and they report similar problems (Geneious 4.6.4 and Codon Code  
> Aligner), so it looks as though something about these ace files is  
> preventing me from reading it.
> 
> Can you help with this problem?
> 
> -----------------------------------------------------------------------------
> 
> 
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-- 
====================================
Björn Nystedt (Sällström)
PhD Student
Molecular Evolution
EBC, Uppsala University
Norbyv. 18C, 752 36  Uppsala
Sweden
phone: +46 (0)18-471 45 88
email: Bjorn.Nystedt@xxxxxxxxx
====================================

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