Question

for FILE in /data/intervals/*.txt; do
    ID=echo ${FILE}
    /data/bin/Tool -a /data/check.txt -b  ${FILE} > /data/final/Outputed_${ID}
done

Giving:

-bash: /data/intervals/CT.BP.200.txt: Permission denied
-bash: /data/final/Outputed_${ID}: ambiguous redirect
-bash: /data/intervals/CT.BP.500.txt: Permission denied
-bash: /data/final/Outputed_${ID}: ambiguous redirect
-bash: /data/intervals/CT.BP.50.txt: Permission denied
-bash: /data/final/Outputed_${ID}: ambiguous redirect
....

etc.

I can’t spot any typo error. Can someone help me with this?

Answer 1

ID=echo ${FILE}

does not do what you think it does. It actually sets the ID environment variable to the value echo then tries to execute ${FILE}, hence the permission denied.

If you want to set ID based on FILE, you need something like one of:

ID=$(echo ${FILE} | sed 'some sed command here')
ID=$(basename ${FILE})

or, if you just want it set to FILE itself:

ID=${FILE}

But, in that case, ID is probably unnecesasary and you can do something like:

for FILE in /data/intervals/*.txt; do
    /data/bin/Tool -a /data/check.txt -b ${FILE} > /data/final/Outputed_${FILE}
done