Has anyone successfully built the human genome db with mpiformatdb? Is there some special gotcha because there are very few, very large sequences (25 sequences in 3 Gb)? I'm using mpiBLAST 1.2.1, with the latest NCBI Toolkit (4 Feb 2004). Other nucleotide dbs build ok with mpiformatdb, but when I try to build the genome in 25 pieces (for 25 sequences), I consistently don't get the 00 piece. i.e. the directory contains #.nsq, #.nin and #.nhr for every piece except 00, where I only see chr_all.fa.00.nin I've tried: - applying the patch (patch-NCBIToolbox_Nov14_2003), just in case, though the docs imply that it is only important for > 100 fragments, so I can't see why it would help in this situation. Only two hunks of the patch 'took'. Still didn't get the missing 00 files. - using an older version of the NCBI Toolkit (Oct 2003). mpiformatdb command: mpiformatdb -f ~/mpiblast.conf -N 25 -i chr_all.fa -p F The formatdb.log says: Version 2.2.8 [Jan-05-2004] Started database file "/fdb/genome/human-aug2003/chr_all.fa" Closing volume /data/susanc/mpiblast//chr_all.fa with 0 sequences, 0 letters(.nsq file = 6158034 0 bytes; .nhr file = 0 bytes) FDBFinish: Empty nucleotide database... Version 2.2.8 [Jan-05-2004] Started database file "/fdb/genome/human-aug2003/chr_all.fa" Closing volume /data/susanc/mpiblast//chr_all.fa.01 with 1 sequences, 246,127,941 letters(.nsq f ile = 122496350 bytes; .nhr file = 67 bytes) Formatted 1 sequences in volume 1 ... We're new to mpiblast (testing it out by user request), so all suggestions appreciated. Susan Chacko. ------------------------------------------------------------------------ ---------------------- Susan Chacko Helix Systems 12B/2N207 Ph: 301-435-2982 National Institutes of Health Fax: 301-402-2190 Bethesda, MD 20814 Email: susanc@nih.gov