[mira_talk] Re: MIRA 3.0.5 error from Assembly::extendADS
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Thu, 06 May 2010 09:17:26 +0200
Hi Bastien,
Just to let you know that I got the same error as Peter reported a few
days ago. Command and last lines of the log are pasted here below. Files
and reads are available at your request. Trying with -DP:ure=no now.
Best,
Lionel
On Thu, 2010-04-22 at 18:08 +0100, Peter wrote:
> in de novo mode I've had a few
> of runs fail as shown below with an error from Assembly::extendADS
> which I don't think has been reported before.
Parsing parameters: --project=m07aNrPeM17 -fasta
--job=denovo,genome,454,sanger,accurate -OUT:ora=yes -GE:not=4
-AS:urd=yes:klrs=no -SK:mmhr=5 454_SETTINGS -CO:mrpg=8:mgqrt=30:mnq=20
[...]
Searching possible read extensions (for Sanger and/or 454):
[0%] ....|Len1: 2789
Len2: 0
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on
http://sourceforge.net/apps/trac/mira-assembler/
"len1 or len2 == 0 ?"
->Thrown: Dynamic::setSequences(const char * seq1, uint32 len1, const
char * seq2, uint32 len2, bool calcwithoffset, int32 expectedoffset)
->Caught: void Assembly::extendADS(int32 version, const string prefix,
const string postfix, const string logname)
Aborting process, 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.
CWD: /seq/m07a/Assembly/m07aNrPeM17
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
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