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You welcome

an12:/home/vbe $ while read LIST; do echo $LIST;sleep 1;done<list
000
00aa
091102
091103
091104
091105
aa
about_dates.howto
about_sa1_sa2_sacd.txt
array001.sh
etc...

I would say its not a good idea to use the same name for a variable and a file when you use both in the same script... (For me it was already confusing...) Then of course there is this syntax error:...

cd $dpath

c=1

newlist=`echo $list | sed 's/.gz//' `
newnewlist=`echo $newlist | sed 's/.fastq//' `

ls -1 $spath | while read LIST
do
echo "$c"
echo $LIST
c=$(($c+1))
done