help on formatdb core dump

gmei at my-dejanews.com gmei at my-dejanews.com
Thu Apr 1 12:45:28 EST 1999


Hi:

I have a genbank datafile (filename:genbankdata) in fasta format that I am
running "formatdb" on.

The file is in directory /data1/genbank/database which is 100GB in size

searchsrv1> ls -l
total 12139628
-rw-r--r--   1 genbank  system          668 Apr  1 11:55 formatdb.log
-rw-r--r--   1 genbank  system   9616926535 Apr  1 08:32 genbank.seq
-rw-r--r--   1 genbank  system   2587447829 Apr  1 09:15 genbankdata


When I run

/data1/program/ncbiblast/formatdb -i genbankdata -p F -o T


It core dumped after about 40 min. And here is the formatdb.log:

========================[ Apr 1, 1999 10:43 AM ]========================
Version 2.0.8 [Jan-05-1999]
Started database file "genbankdata"
FATAL ERROR: CoreLib [001.000] Failed to allocate 62768120 bytes


And I looked the disk space:

searchsrv1> df -k Filesystem  1024-blocks  Used  Available Capacity  Mounted
on root_domain#root  532176  66362  458776  13%  / /proc  0  0	0  100% 
/proc usr_domain#usr  4147848  536348  3576896	14%  /usr
search_domain#programs	17780000  16  17773576	1%  /programs
search1_domain#data1  106665000  21567728  85067880  21%  /data1


And idea where is source of error?

If you reply, please send a copy to gmei at pavonis.com

Thanks.


Guang Mei

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