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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