[mira_talk] Re: Call for testing: MIRA 3.2.1.17 and Ion Torrent
- From: Tony Travis <a.travis@xxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 16 May 2011 14:12:57 +0100
On 16/05/11 13:21, Bastien Chevreux wrote:
*> From:* Phillip San Miguel
> Looks like a parameter parsing bug has crept in?
> nohup mira -DIR:lrt=/scratch/pmiguel/ --project=TL3360
--job=denovo,genome,accurate,solexa
> SOLEXA_SETTINGS -GE:tismin=200:tismax=700 > & ! log_assembly
> works fine for MIRA V3.2.1.15. but errors out with MIRA V3.2.1.17.
Ooops ... no bug, but forgot to put that in the CHANGES file (and update
the docs):
The "log" directory is no more, long live the "tmp" directory.
Hi, Bastien.
Should that not be the /var/tmp directory?
Typically, /tmp is 'small', fast' and volatile; /var/tmp is 'large', not
so fast, but persistent across reboots.
My three-week(!) MIRA assembly of 20x106 paired-end Solexa + 270x104 454
reads has just crashed when you announced your call for testing ;-)
Maybe someone is trying to tell me something?
I've just tried your development version, but it crashed:
mira -project=meta \
-job=denovo,genome,normal,sanger,454,solexa \
COMMON_SETTINGS -GE:not=16 -SK:nrr=100 \
SANGER_SETTINGS -GE:tismin=5000:tismax=40000 -LR:lsd=on,ft=fasta
-CL:msvs=yes \
454_SETTINGS -LR:lsd=on,ft=fasta -CL:msvs=yes \
SOLEXA_SETTINGS -GE:tismin=160:tismax=220 -LR:lsd=on,ft=fasta
-CL:msvs=yes
> [...]
Internal logic/programming/debugging error (*sigh* this should not have
happened).
Please file a bug report on http://sourceforge.net/apps/trac/mira-assembler/
"While trying to set the name of read
<trace>
Encountered character with ASCII code 32. T
It is probably due to your input data, but normally, MIRA should have caught that
earlier!"
->Thrown: void Read::setName(const string & name)
->Caught: main
Aborting process, probably due to an internal error.
Bye,
Tony.
In fact, the contents are currently exactly the same, it's just been
renamed to reduce the number of question like in "can I delete contents
of the log directory during a run, they're so big". (Answer: for most,
no, you cannot).
Consequently, I also had to rename a couple of parameters to keep naming
consistent. -DIR:lrt is one of these. It's new name is ... "-DIR:trt".
Use that and all should be good.
I'm sorry for the confusion that this will create during a (hopefully)
short transition period.
Best,
Bastien
--
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis@xxxxxxxxxx, http://bioinformatics.rri.sari.ac.uk
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