[Bioclusters] (no subject)

kenix y bioclusters@bioinformatics.org
Tue, 20 Jul 2004 09:21:17 +0800

Yes, I did. I ran /opt/BioBrew/NCBI/6.1.0/bin/mpiformatdb -f 
/home/bigcpuguest/mpiblast.conf -N 2 -i ecoli.nt -o T -p F

Trying to break ecoli.nt (5MB) into 3 fragments of 2 MB
Executing: formatdb -i ecoli.nt -o T -p F -v 2

Moving fragments to /mnt/pvfs
mv: cannot stat 'ecoli.nt.nal': No such file or directory
Created and moved 3 fragments.

The only files produced in /mnt/pvfs is
ecoli.nt.00.nhr    ecoli.nt.01.nhr    ecoli.nt.02.nhr
ecoli.nt.00.nin    ecoli.nt.01.nin     ecoli.nt.02.nin
ecoli.nt.00.nnd   ecoli.nt.01.nnd    ecoli.nt.02.nnd
ecoli.nt.00.nni    ecoli.nt.01.nni     ecoli.nt.02.nni
ecoli.nt.00.nsd    ecoli.nt.01.nsd    ecoli.nt.02.nsd
ecoli.nt.00.nsi     ecoli.nt.01.nsi     ecoli.nt.02.nsi
ecoli.nt.00.nsq    ecoli.nt.01.nsq    ecoli.nt.02.nsq
ecoli.nt.dbs        (null).nal

The index files are in /mnt/pvfs, seven of  them.
I do not know what else is missing, is it something to do with ecoli.nt.nal?

>From: Glen Otero <gotero@linuxprophet.com>
>Reply-To: bioclusters@bioinformatics.org
>To: bioclusters@bioinformatics.org
>Subject: Re: [Bioclusters] (no subject)
>Date: Mon, 19 Jul 2004 08:11:03 -0700
>Did you run formatdb (mpiformatdb) in /mtn/pvfs? That will create the index 
>On Jul 18, 2004, at 11:32 PM, kenix y wrote:
>>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 
>>After I did, I got this:
>>[blastall] WARNING: ftsYRP,: Could not find index files for database 
>>[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.

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