[Bioclusters] [mpiBLAST]how to "mpiformatdb nr"~~?THX~
kwLee
bioclusters@bioinformatics.org
Wed, 14 May 2003 16:49:36 +0800
This is a multi-part message in MIME format.
------=_NextPart_000_0008_01C31A38.CD81EA40
Content-Type: text/plain;
charset="big5"
Content-Transfer-Encoding: quoted-printable
thx~John~
i mpiformat nr again
and the message as follow:
>Breaking up /home/ct/toolkit/mpiBLAST-1.0.1/nr (458.894995 MB) into 8 =
>fragments of 57.361874375 MB
>/home/ct/toolkit/ncbi/bin/formatdb -i nr -v 57.361874375 -p T -o T: =
exit status: 0
>Moving fragments to /home/ct/toolkit/mpiBLAST-1.0.1
>ls: /home/ct/toolkit/mpiBLAST-1.0.1/nr.*.nsq: No such file or directory
>You must create at least two fragments to use mpiblast.
so i guess that there is some problem in the file "mpiblast.conf"
i set "mpiblast.conf" as follow
>/home/ct/toolkit/mpiBLAST-1.0.1
>/home/ct/toolkit/mpiBLAST-1.0.1
>/home/ct/toolkit/ncbi/bin
in fact=20
i believe i didn't installed mpiBLAST correctly
because when i use "mpiblast blastn" to search "yeast.nt" every time
there are some error message like this
>cp: `/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.00.nhr' and =
`/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.00.nhr' are the same file
>cp: `/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.00.nin' and =
`/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.00.nin' are the same file
>..
>..
>cp: `/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.07.nsi' and =
`/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.07.nsi' are the same file
>[blastall] WARNING: test2: Could not find taxdb.bti
but i can get the search result
anybody could solve these problems?
thanks a lot~: )
-Lee
------=_NextPart_000_0008_01C31A38.CD81EA40
Content-Type: text/html;
charset="big5"
Content-Transfer-Encoding: quoted-printable
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; charset=3Dbig5">
<META content=3D"MSHTML 6.00.2600.0" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV>thx~John~</DIV>
<DIV>i mpiformat nr again</DIV>
<DIV>and the message as follow:</DIV>
<DIV>>Breaking up /home/ct/toolkit/mpiBLAST-1.0.1/nr (458.894995 MB) =
into 8=20
>fragments of 57.361874375 =
MB<BR>>/home/ct/toolkit/ncbi/bin/formatdb =20
-i nr -v 57.361874375 -p T -o T: exit status: 0<BR>>Moving fragments =
to=20
/home/ct/toolkit/mpiBLAST-1.0.1<BR>>ls:=20
/home/ct/toolkit/mpiBLAST-1.0.1/nr.*.nsq: No such file or =
directory<BR>>You=20
must create at least two fragments to use mpiblast.<BR>so i guess that =
there is=20
some problem in the file "mpiblast.conf"</DIV>
<DIV>i set "mpiblast.conf" as follow</DIV>
<DIV>>/home/ct/toolkit/mpiBLAST-1.0.1<BR>>/home/ct/toolkit/mpiBLAST=
-1.0.1<BR>>/home/ct/toolkit/ncbi/bin<BR>in=20
fact </DIV>
<DIV>i believe i didn't installed mpiBLAST correctly</DIV>
<DIV>because when i use "mpiblast blastn" to search "yeast.nt" every =
time</DIV>
<DIV>there are some error message like this</DIV>
<DIV>>cp: `/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.00.nhr' and=20
`/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.00.nhr' are the same=20
file<BR>>cp: `/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.00.nin' =
and=20
`/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.00.nin' are the same =
file</DIV>
<DIV>>..</DIV>
<DIV>>..</DIV>
<DIV>>cp: `/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.07.nsi' and=20
`/home/ct/toolkit/mpiBLAST-1.0.1/src/yeast.nt.07.nsi' are the same=20
file<BR>>[blastall] WARNING: test2: Could not find taxdb.bti</DIV>
<DIV>but i can get the search result</DIV>
<DIV><SPAN class=3D758550920-13052003>anybody could solve these=20
problems?</SPAN></DIV>
<DIV><FONT size=3D2>thanks a lot~: )</FONT></DIV>
<DIV> </DIV>
<DIV><FONT size=3D2>-Lee</FONT></DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV></BODY></HTML>
------=_NextPart_000_0008_01C31A38.CD81EA40--