It seems that my earlier error was due to the fact that I forgot to change the permission of /tmp/blast of my compute node, sorry for my absent-mindedness. After I did, I got this: [blastall] WARNING: ftsYRP,: Could not find index files for database /mnt/pvfs/ecoli.nt [blastall] WARNING: ftsYRP,: polARP,: Could not find index files for database /mnt/pvfs/ecoli.nt [blastall] WARNING: ftsYRP,: polARP,: metKRPB,: Could not find index files for database /mnt/pvfs/ecoli.nt [blastall] WARNING: ftsYRP,: polARP,: metKRPB,: dnaERP,: Could not find index files for database /mnt/pvfs/ecoli.nt I do have the index files (.nhr, .nin, .nsq, .nsd, .nsi, .nni, .nnd) in /mnt/pvfs, what else can I do? Thank you. _________________________________________________________________ Get 10mb of inbox space with MSN Hotmail Extra Storage http://join.msn.com/?pgmarket=en-sg