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-bash-3.00$ grep --version
grep (GNU grep) 2.5.1

Copyright 1988, 1992-1999, 2000, 2001 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO...

en, this is what i have run on my machine (FC9)

-bash-3.00$ cat xxx.txt
chr1 3821 rs127372 A/C 0.823
chr1 3822 rs127376 A/C/G 0.899
chr1 3722 rs612634 A/C 9.22
chr1 3262 rs7152 A/T 0.22
chr1...

#! /bin/bash

echo $?
su user
echo $?
the running result is,

-bash-3.00$ ./su.sh
0
su: user user does not exist
1
$? can be helpful?

How about
grep "A/C " xxx.txt
? there is a space after "C"

How about make the scp process running in the background? use the '&'

Like this,
scp -p $SOURCEFILE ${server}:$TARGETDIR &