[mira_talk] Re: hybrid assembly crashes - file not found

Bastien Chevreux wrote:

On Monday 09 March 2009 Andreas Petzold wrote:

[...]
Before I kept all my experiment files in one separate folder and the "files
to assemble" contained the correct paths. Now I started the assembly in the
folder with the experiment files and everything seems to work fine ...
I can't explain why but maybe you could try something for further
debbuging: Make a assembly of 1000 (or more) experiment files that lie in
another folder .... :-)


Hi Andreas,
sorry for the late reply, just came back from the VAAM 2009 conference where I had a short talk on sequencing and reseqeucnings and what nice thing one can do with hybrid data sets.
Awkward problem you have there. I also used that tactic earlier, but then switched to "just the filenames" in the fofn and setting a master directory name via "-DIR:exp=..." (before completely switching to FASTA + XML). I haven't used the path+filename in fofn since quite some time, perhaps something broke without me noticing.
I've taken it up on the TODO list, medium priority as you found a workaround, but would switch to "high" if you need it badly. Loading data should be something which works without crashing *sigh* 

Regards,
  Bastien





Hi Bastien,

nah, assembly is working fine. Thus I think it has rather low priority for me. 
And I hope
I don't have to assemble 200000 experiment files again in the next future. 
But this is one of the many problems you encounter when switching from mere 
Sanger sequencing
to massive 454 and Solexa sequencing.

Thanks and greets,
Andreas 

--

Andreas Petzold
Genome Analysis
Fritz Lipmann Institute
Beutenbergstrasse 11, D-07745 Jena
voice : ++49-3641-656488
fax   : ++49-3641-656488
email : andpet@xxxxxxxxxxxxxx

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