[Bioclusters] My mpiformatdb can't format NCBI nt DB
alfalf
bioclusters@bioinformatics.org
Tue, 27 May 2003 16:16:48 +0900
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Hi.
I successfully compiled mpiblast in RedHat Linux environment with gcc
version 3.2.
But, When I perform mpiformatdb with nt sequence (about 8.4 GB), =
mpiformatdb
print "Error: Unable to open nt" and quit.
For more information, I perform strace with full command.
=20
..
open("/root/.mpiblastrc", O_RDONLY) =3D -1 ENOENT (No such file or
directory)
open("/share/mpiblast/etc/mpiblast.conf", O_RDONLY) =3D 3
brk(0) =3D 0x82db000
brk(0x82dd000) =3D 0x82dd000
fstat64(3, {st_mode=3DS_IFREG|0644, st_size=3D48, ...}) =3D 0
mmap2(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, =
0) =3D
0x40014000
read(3, "/path/to/shared/storage\n/path/to"..., 8192) =3D 48
read(3, "", 4096) =3D 0
close(3) =3D 0
munmap(0x40014000, 4096) =3D 0
open("nt", O_RDONLY) =3D -1 EFBIG (File too large)
write(2, "E", 1E) =3D 1
write(2, "r", 1r) =3D 1
write(2, "r", 1r) =3D 1
write(2, "o", 1o) =3D 1
write(2, "r", 1r) =3D 1
write(2, ":", 1:) =3D 1
..
write(2, "\n", 1
) =3D 1
_exit(-1) =3D ?
=20
I think that is large file problem. How I can perform mpiformatdb with =
large
file?
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<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>Hi</span></font><font =
face=3DArial><span
lang=3DEN-US style=3D'font-family:Arial'>…</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>I successfully compiled =
mpiblast in RedHat
Linux environment with gcc version 3.2.</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>But, When I perform =
mpiformatdb with
nt sequence (about 8.4 GB), mpiformatdb print </span></font><font =
face=3DArial><span
lang=3DEN-US style=3D'font-family:Arial'>“</span></font><font =
face=3D굴림><span
lang=3DEN-US style=3D'font-family:Gulim'>Error: Unable to open =
nt</span></font><font
face=3DArial><span lang=3DEN-US =
style=3D'font-family:Arial'>”</span></font><font
face=3D굴림><span lang=3DEN-US style=3D'font-family:Gulim'> =
and quit.</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>For more information, I =
perform strace
with full command.</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-US =
style=3D'font-size:
10.0pt;font-family:Arial'>……</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>open("/root/.mpiblastrc=
",
O_RDONLY) =3D -1 ENOENT (No such file or =
directory)</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>open("/share/mpiblast/e=
tc/mpiblast.conf",
O_RDONLY) =3D 3</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>brk(0) &nbs=
p;  =
; =
=3D 0x82db000</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>brk(0x82dd000) &n=
bsp; &nb=
sp;
=3D 0x82dd000</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>fstat64(3, =
{st_mode=3DS_IFREG|0644, st_size=3D48,
...}) =3D 0</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>mmap2(NULL, 4096,
PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) =3D =
0x40014000</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>read(3,
"/path/to/shared/storage\n/path/to"..., 8192) =3D =
48</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>read(3, "",
4096) &n=
bsp;
=3D 0</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>close(3) =
&=
nbsp; &n=
bsp; =3D
0</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>munmap(0x40014000,
4096) &n=
bsp;
=3D 0</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>open("nt",
O_RDONLY) &nbs=
p;
=3D -1 EFBIG (File too large)</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DPT-BR
style=3D'font-size:10.0pt;font-family:Gulim'>write(2, "E",
1E) &nbs=
p;
=3D 1</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DPT-BR
style=3D'font-size:10.0pt;font-family:Gulim'>write(2, "r",
1r) &nbs=
p;
=3D 1</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DPT-BR
style=3D'font-size:10.0pt;font-family:Gulim'>write(2, "r",
1r) =
&=
nbsp; =3D
1</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DPT-BR
style=3D'font-size:10.0pt;font-family:Gulim'>write(2, "o",
1o) &nbs=
p;
=3D 1</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>write(2, "r",
1r) &nbs=
p;
=3D 1</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>write(2, ":",
1:) &nbs=
p;
=3D 1</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3DArial><span lang=3DEN-US =
style=3D'font-size:
10.0pt;font-family:Arial'>……</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>write(2, "\n", =
1</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>) &nb=
sp; &nbs=
p;
=3D 1</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>_exit(-1) &=
nbsp; &n=
bsp; &nb=
sp;
=3D ?</span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'> </span></font></p>
<p class=3DMsoNormal><font size=3D2 face=3D굴림><span =
lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Gulim'>I think that is large file =
problem. How
I can perform mpiformatdb with large file?</span></font></p>
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