help on formatdb core dump

[Jonathan Epstein]

Your root file system is full.  This is probably where your system's
temporary space is allocated.  Delete some stuff, especially from /tmp
and /var/tmp, and try again.

You may be more successful if you set your TMPDIR environment variable
to point to a directory on your large /data1 file system prior to
rerunning BLAST.  This should direct BLAST to place its temporary files
there, which might help.

- Jonathan

gmei at my-dejanews.com wrote:
> 
> 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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