Dear Corona688,
Thank you for your reply. I incorporated the changes but it seems its not able to find the data file ( although i put explicit path name).
Below is the code and error:
Code:
#!/bin/bash
cat <<EOF > data.txt
auto
n
/home/multalign/tab/dna.tab
n
msf
y
aligned
100.90
EOF
#for x in {A..H}
for x in H
do
echo $x
for y in PreS1 PreS2 S X
do
/home/multalign/tab/ma ${x}_${y}.fas < data.txt
echo Done: ${x}_${y}.fas
done
done
Error:
Code:
H
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_PreS1.fas
Sequence # 30
Error: Error reading blosum62.tab.
Done: H_PreS1.fas
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_PreS2.fas
Sequence # 30
Error: Error reading blosum62.tab.
Done: H_PreS2.fas
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_S.fas
Sequence # 72
Error: Error reading blosum62.tab.
Done: H_S.fas
Multalin version 5.4.1
Copyright I.N.R.A. France 1989, 1991, 1994, 1996
Published research using this software should cite
Multiple sequence alignment with hierarchical clustering
F. CORPET, 1988, Nucl. Acids Res., 16 (22), 10881-10890
Reading H_X.fas
Sequence # 26
Error: Error reading blosum62.tab.
Done: H_X.fas
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Discussion started by: kidi
7 Replies
LEARN ABOUT NETBSD
fincore
FINCORE(1) BSD General Commands Manual FINCORE(1)NAME
fincore -- query in-core status of file pages
SYNOPSIS
fincore [-qs] file ...
DESCRIPTION
The fincore utility queries and displays in-core status of specified files.
Note that the result can already be stale when being output due to other activities in the system. Thus it should be used only for advisory
purposes.
The fincore utility accepts the following options.
-q The quiet mode. Outputs nothing unless the file has in-core pages.
-s The summary mode. Only shows number of pages.
EXAMPLES
The following example shows that /bin/cat and /bin/cp are fully cached in-core while the other executables are not in-core. numbers shown in
the default output are page indexes in the file of each in-core pages.
% fincore /bin/c*
/bin/cat: 0 1 2 3
/bin/chio:
/bin/chmod:
/bin/cp: 0 1 2 3 4 5
/bin/cpio:
/bin/csh:
% fincore -s /bin/c*
/bin/cat: 4 / 4 in-core pages (100.00%)
/bin/chio: 0 / 5 in-core pages (0.00%)
/bin/chmod: 0 / 3 in-core pages (0.00%)
/bin/cp: 6 / 6 in-core pages (100.00%)
/bin/cpio: 0 / 36 in-core pages (0.00%)
/bin/csh: 0 / 41 in-core pages (0.00%)
SEE ALSO mincore(2)AUTHORS
The fincore utility is written by YAMAMOTO Takashi.
CAVEATS
The concept of page cache is an implementation detail of the kernel. The fincore utility works using some assumptions on the current imple-
mentation. Thus it might stop working in a future version of NetBSD.
BUGS
The amount of CPU time the current implementation of fincore utility would take is roughly proportional to the file sizes. Ideally it should
be proportional to the number of in-core pages.
BSD January 5, 2012 BSD