[mira_talk] FW: 454 assembly
- From: "Shabhonam Caim (TGAC)" <Shabhonam.Caim@xxxxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 22 Jul 2010 09:53:40 +0100
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.
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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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