[mira_talk] Re: FW: 454 assembly
- From: Thomas Müller <thomas.mueller@xxxxxxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 22 Jul 2010 11:12:25 +0200
try:
mira --project=test --job=denovo,genome,draft,est 454_SETTINGS
-FN:fai=2.GAC.454Reads.fna
But you should really also add the .qual file with FN:fqui=2.GAC.454Reads.qual
cheers
Thomas
On Jul 22, 2010, at 10:53 AM, Shabhonam Caim (TGAC) wrote:
>
> Hello Mira Users
>
> I am trying to assemble the 454 reads using Mira by using following command:
> mira-3.0.0 mira --project=test --job=denovo,genome,draft,2.GAC.454Reads.fna
>
> and I am getting the following error:
>
> This is MIRA V3.0.0 (production version).
>
> Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
> Assembly Using Trace Signals and Additional Sequence Information.
> Computer Science and Biology: Proceedings of the German Conference on
> Bioinformatics (GCB) 99, pp. 45-56.
>
> Mail general questions to the MIRA talk mailing list:
> mira_talk@xxxxxxxxxxxxx
>
> To (un-)subsubcribe the MIRA mailing lists, see:
> http://www.chevreux.org/mira_mailinglists.html
>
> To report bugs or ask for features, please use the new ticketing system at:
> http://sourceforge.net/apps/trac/mira-assembler/
> This ensures that requests don't get lost.
>
>
> Compiled by: bach
> Sun Jan 31 20:23:36 CET 2010
> On: Linux arcadia64 2.6.27-11-generic #1 SMP Wed Apr 1 20:53:41 UTC 2009
> x86_64 GNU/Linux
> Compiled in boundtracking mode.
> Compiled in bugtracking mode.
> Compilation settings (sorry, for debug):
> Size of size_t : 8
> Size of uint32 : 4
> Size of uint32_t: 4
> Size of uint64 : 8
> Size of uint64_t: 8
> Current system: Linux n57140 2.6.18-92.el5 #1 SMP Tue Apr 29 13:16:15 EDT
> 2008 x86_64 x86_64 x86_64 GNU/Linux
>
>
>
> Parsing parameters: --project=454asembly --job=denovo, genome, draft
> pk.454.fasta
>
> Seen no assembly quality in job definition, assuming 'normal'.
> Seen no assembly type in job definition, assuming 'genome'.
>
> ,..
>
> ========================= Parameter parsing error(s)
> ==========================
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: genome
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: draft
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: pk
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: 454
>
> * Parameter section: '(none)'
> * unrecognised string or unexpected character: fasta
>
> ===============================================================================
>
> Fatal Error (may be due to problems of the input data):
> "Error while parsing parameters, sorry."
>
> ->Thrown: void MIRAParameters::parse(istream & is, vector<MIRAParameters> &
> Pv, MIRAParameters * singlemp)
>
> ->Caught: main
>
> Or can I please get the commands to run the 454 assembly (basic denovo
> assembly with default parameters)
>
> cheers
>
> Shab
>
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