[mira_talk] running Mira on pair-end Illumina data
- From: Maely Gauthier <m.gauthier@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Mon, 14 Jul 2014 01:48:15 +0000
Hi there,
I am using a server on which Mira V3.4.1.1 is installed as a module.
I can run the following command:
mira --project=Mira_project --job=genome,denovo,accurate,solexa
--fastq=Mira_project/Mira_project.2.fq -DI:trt=/scratch | tee log_assembly.txt
However I am not sure how to modify it to specify pair-end data?
As an alternative, I am trying to run mira using a manifest file but it does
not seem to get recognised as a correct parameter, whether it is located in the
directory from which I run the mira command, or specify the path to it, or
place it in my home dir
mira manifest_conf
I get the following error message:
This is MIRA V3.4.1.1 (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
Wed Nov 14 23:07:20 CET 2012
On: Linux vk10464 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC 2012
x86_64 GNU/Linux
Compiled in boundtracking mode.
Compiled in bugtracking mode.
Compiled with ENABLE64 activated.
Runtime 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 b07b07 3.0.80-0.5-default #1 SMP Fri May 31 20:04:37 UTC
2013 (f5a0e1f) x86_64 x86_64 x86_64 GNU/Linux
Parsing parameters: manifest_conf
========================= Parameter parsing error(s) ==========================
* Parameter section: '(none)'
* unrecognised string or unexpected character: manifest_conf
===============================================================================
Fatal error (may be due to problems of the input data or parameters):
"Error while parsing parameters, sorry."
->Thrown: void MIRAParameters::parse(istream & is, vector<MIRAParameters> & Pv,
MIRAParameters * singlemp)
->Caught: main
Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see:
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CWD: /ebi/bscratch/uqmgauth/sponge/multi-metagenome/reassembly/20140710
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Thanks in advance for any tips or advice
M
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