[mira_talk] Re: MIRA to Gap4/5
- From: Jeremiah Davie <jdavie@xxxxxxxxxxx>
- To: <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 9 Jul 2010 11:43:17 -0400
Hi Sonia,
I can't speak to all of you questions, but I believe I the reason your Gap5
database doesn't have MIRA tags is because the ACE specification doesn't keep
those tags. I wish could give you a solution, but I can at least provide an
explanation. Best wishes! - Jeremiah
On Fri 07/09/10 10:40 AM , Sònia Casillas sonia.casillas@xxxxxxx sent:
> Hi,
>
> I'm trying to visualize a MIRA assembly with Gap4 and Gap5 (Staden
> Package version 2.0.0b6). However I have the following problems even
> after using convert_project to exclude contigs shorter than 500 bases
> and with a coverage smaller than 1/3 the average coverage:
>
> - For Gap4, I use the program caf2gap (from CAFTOOLS version 2.0.2) to
> convert the MIRA CAF assembly into a Gap4 database, but I get the error
> "!! FATAL ERROR: system error 12 Cannot allocate memory !! Memory
> allocation failure when requesting -2147483648 bytes Aborted". I have
> a hybrid 454/Sanger assembly of 4,007,215 reads, and work in an Ubuntu
> 64bits Server with 64 GiB RAM. RAM is not completely used when I get the
> error.
>
> - For Gap5, I use the ACE file from MIRA to create the Gap5 database
> using tg_index, but Gap5 doesn't display any MIRA tags :-( Now I'm
> trying to convert the CAF file from MIRA to BAF using the script
> caf2baf.pl from the Staden Package with the idea to create the Gap5
> database from the BAF file and see if it displays MIRA tags, but it's
> been running for more than one day now...
>
> Do you have any idea? Maybe run again MIRA and ask MIRA to output the
> assembly in gap4da format?
>
> Now I have to apologize for asking something a bit out of this list, but
> have any of you been able to compile BAMBUS in an Ubuntu 10.04? I can't
> manage to compile it either in 32 or a 64 bits, even when changing the
> files in the manual distributed with MIRA, and the AMOS mailing list is
> not responding at all. Any help will be greatly appreciated.
>
> Thank you very much in advance, and thanks a lot Bastien for your
> response to my first question in this mailing list.
>
> Best regards,
> Sònia
>
>
>
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