[mira_talk] Re: mira 3.9 manifest file for hybrid assembly
- From: Marcelo Brandão <brandao.marcelo@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 12 Oct 2012 15:16:53 -0600
Hello Bastien
Here is the output. I am using RocksCluster version 5.5
Your system seems to be older or have some quirks with locale settings.
Using the LC_ALL=C workaround.
If you don't want that, upgrade your system ;-)
This is MIRA 3.9.4 ().
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
Sat Aug 25 23:15:51 CEST 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 thunder-0-4.local 2.6.18-308.4.1.el5 #1 SMP Tue Apr
17 17:08:00 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux
k: project
v: Mira_SBW_Map3
k: job
v: mapping,genome,accurate,solexa
k: parameters
v: -GE:not=15
k: readgroup
v: 454assembly
k: technology
v: 454
k: data
v: Mira_SBW_Map3_backbone_in.caf
k: as_reference
v:
k: parameters
v: -SB:bft=caf
k: -SK:mnr
v: 1:pr=70:hss=2
Fatal error (may be due to problems of the input data or parameters):
"In file ../map3_manifest.dat: line
-SK:mnr=1:pr=70:hss=2
has keyword '-sk:mnr' which is not recognised."
->Thrown: void Manifest::slurpInManifest(stringstream & mfin, const string
& origsource))
->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.
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CWD: /thunderstorm/users/mmbrand/C_fumiferana/assembly/mira/Map3
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Thank you very much.
Marcelo
--
Marcelo Mendes Brandão
Academic Visitor at University of Alberta @ Edmonton
Website: http://bioinfo.esalq.usp.br
AtPIN: http://bioinfo.esalq.usp.br/atpin
SKYPE: mmbrand
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