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

YOU NEED TO WRITE :   consed -nophd -ace







-----Original Message-----
From: mira_talk-bounce@xxxxxxxxxxxxx
[mailto:mira_talk-bounce@xxxxxxxxxxxxx] On Behalf Of Bastien Chevreux
Sent: Sunday, May 10, 2009 10:49 AM
To: mira_talk@xxxxxxxxxxxxx
Subject: [mira_talk] Fwd: ace file output from MIRA

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

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[...]

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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