[mira_talk] Re: MIRA->Some good editor
- From: Bastien Chevreux <bach@xxxxxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 15 Jul 2011 21:23:19 +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)
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:
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.
> 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.
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