[Bioperl-l] blastall call --- cannot find index files for databases
Liu Haifeng
lhaifeng@dso.org.sg
Fri, 3 May 2002 15:46:49 +0800
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Hi,
I just met another problem. I have used "formatdb -o T ..." to =
construct one protein database "mydbname" whose defline is like =
"gnl|sth|sthelse". It is ok if I directly perform blastall query in my =
linux console window. Howvever, if I perform a perl script which uses =
Bio::Tools::Run::StandAloneBLast to call blastall, then the program =
always crashes and shows "WARNING: Could not find index files for =
database mydbname ...". I have set $BLASTDATADIR in my .bashrc file.
Could anyone help me to solve the problem?
Regards
Haifeng =20
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Haifeng Liu
Ph.D., Member of Technical Staff
IFL/DS
DSO National Laboratories
20 Science Park Drive
Singapore 118230
Email: lhaifeng@dso.org.sg
Tel: (65) 67728220
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<DIV><FONT face=3DArial size=3D2>Hi,</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=3DArial size=3D2>I just met another problem. I =
have used=20
"formatdb -o T ..." to construct one protein database "mydbname" whose =
defline=20
is like "gnl|sth|sthelse". It is ok if I directly perform blastall =
query=20
in my linux console window. Howvever, if I perform a perl =
script=20
which uses Bio::Tools::Run::StandAloneBLast to call blastall,=20
then the program always crashes and shows "WARNING: Could =
not=20
find index files for database mydbname ...". I have=20
set $BLASTDATADIR in my .bashrc file.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Could anyone help me to solve the=20
problem?</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT> </DIV>
<DIV><FONT face=3DArial size=3D2>Regards</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Haifeng </FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=3DArial =
size=3D2>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<BR>Haifeng=20
Liu<BR>Ph.D., Member of Technical Staff</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=3DArial size=3D2>IFL/DS<BR>DSO National =
Laboratories<BR>20 Science=20
Park Drive<BR>Singapore 118230</FONT></DIV>
<DIV> </DIV>
<DIV><FONT face=3DArial size=3D2>Email: <A=20
href=3D"mailto:lhaifeng@dso.org.sg">lhaifeng@dso.org.sg</A><BR>Tel: (65) =
67728220<BR>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</FONT></DIV></BODY></HTML>
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