[mira_talk] MIRA to Gap4/5
- From: Sònia Casillas <sonia.casillas@xxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 09 Jul 2010 16:40:28 +0200
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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