[mira_talk] Re: Internal logic/programming/debugging error
- From: Jan Paces <hpaces@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 26 Mar 2010 14:19:18 +0100
On 03/24/10 00:13, Bastien Chevreux wrote:
> http://www.chevreux.org/tmp/mira_3.0.3x2_prod_linux-gnu_x86_64_static.tar.bz2
This version of mira crashed here, excerpt from log follows. Should I
fill the bug report?
------------------------------------------------
This is MIRA V3.0.3x2 (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.
-------------------------------------------------
Compiled by: bach
Mon Mar 22 00:05:24 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 cheetah 2.6.24-27-server #1 SMP Fri Mar 12
01:23:09 UTC 2010 x86_64 GNU/Linux
Parsing parameters: -projectin=mas -projectout=mi_v13
-job=denovo,genome,454,normal -CO:np=a13 COMMON_SETTINGS -GE:not=12
--------------------------------------------------
Localtime: Fri Mar 26 13:03:25 2010
Counting number of alignments in file ... done.
Expecting 173680014 alignments.
Localtime: Fri Mar 26 13:03:58 2010
Loading confirmed overlaps from disk (will need approximately 9.7 GiB RAM):
[0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%]
....|.... [90%] ....|....
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/
"Error while loading adsfacts, more facts in file than calculated
earlier! (173680014)"
->Thrown: void Assembly::loadAlignmentsFromFile(int32 version, const
string prefix, const string postfix, const string logname)
->Caught: void Assembly::loadAlignmentsFromFile(int32 version, const
string prefix, const string postfix, const string logname)
Program aborted, probably due to an internal error.
If you want to report the error, please do so on
http://sourceforge.net/apps/trac/mira-assembler/
and also give a short notice on the mira talk mailing list.
If reporting, please do not delete the log and checkpoint directories,
there may
be files in them which could be needed to find the problem.
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