[mira_talk] Re: IUPAC consensus
- From: Rob Syme <rob.syme@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Sat, 31 Aug 2013 13:27:24 +0800
> Guess what? This was exactly what I initially developed the mapping for :-)
>
Fantastic! I'm glad I'm not on the wrong track.
You'd be surprised what short reads can tell you about collapsed repeats in
> your reference sequence. If you haven't done so yet, look at the data in a
> finishing tool (gap5, but configure it so that it knows the MIRA tags (and
> that you can search for them)). Go on the hunt for SNPs there as well as
> coverage plots in wiggle.
>
> But hey, it's your call, you can do what you want.
>
> Then again … you want to check, believe me.
>
> Am I nagging too much? :-)
>
Ha. Ok, I promise I'll look at the tags.
>
> http://www.chevreux.org/tmp/mira_develop-0-ga60f09d_linux-gnu_x86_64_static.tar.bz2
>
>
Thanks Bastien. Using the old maf (linked earlier in the thread), I ran
using the new binaries:
miraconvert -f maf -t fasta -r C MIRA_run7_out.maf test
Miraconvert gets about 95% of the way through but falls just short of the
line with:
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: index (1) >= RC_poolrptr.size() (1) ?
*
*******************************************************************************
->Thrown: Read & ReadContainer::getRead(uint32 index)
->Caught: void MAFParse::parseLineEC(ifstream & mafin, string & acttoken,
string & actline)
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.
Subscribing / unsubscribing to mira talk, see:
//www.freelists.org/list/mira_talk
CWD: /data/rob/tmp/MIRA/run7/MIRA_run7_assembly/MIRA_run7_d_results
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Was the fix only with the miraconvert, or should I generate a fresh
assembly with the new binaries?
Thanks again Bastien.
-r
Other related posts:
