[mira_talk] Re: MIRA->Some good editor
- From: Nestor Zaburannyi <nestor@xxxxxxxxxxxxx>
- To: Bastien Chevreux <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 15 Jul 2011 21:43:41 +0200
> On Jul 15, 2011, at 18:03 , Nestor Zaburannyi wrote:
>> Why is .gap4da output not recommended nor created anymore? From the first
>> day of my MIRA usage, i can not convert my projects into Gap4, because of
>> !! FATAL ERROR: system error 12 Cannot allocate memory
>> !! Memory allocation failure when requesting -2147483648 bytes
> Uh oh ... you must have quite some large result projects.
> You have exactly 2.5 options left I think:
> 0.5: You write a bug report to the authors of caf2gap (you might want to do
> that anyway)
If only i could find them :)
> 1.5: split the MIRA result into smaller parts to be worked on individually in
> gap4. You might for example want to try the "-s" option of convert_project to
> split by contigs:
I will try that one.
> convert_project -f maf -t caf -s mira_output.maf mysplit
> 2.5: you scrap gap4 and use gap5. To input the project into gap5 use:
> tg_index -C mira_out.caf
> where tg_index is a tool supplied by the gap5 package.
This always works, but gap5 lacks many of the gap4 features.
>> Also, convert_project for "-t gap4da" is not available nowadays, too?
> In convert_project, it's called "-t exp".
> WARNING WARNING WARNING RED ALERT WARNING WARNING WARNING
> Do not do that with projects containing more than a couple of hundred
> thousand reads. That format implies that in a single directory, one file is
> created on disk for each and every read ... and your filesystem will not like
> that.
> You. Have. Been. Warned ;-)
> B.
Regards
Nestor
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