Renaming multiples files with a bash loop

Several mistakes here:

NEWNAME = should be without space. Here bash is looking for a command named NEWNAME and that fails.
you parse the output of ls. this is bad if you had files with spaces. Bash can build itself a list of files with the glob operator *.
You don't escape "$i" and "$NEWNAME". If any of them contains a space it makes two arguments for mv.
If a file name begins with a dash mv will believe it is a switch. Use -- to stop argument processing.

Try:

for i in chr*do  mv -- "$i" "${i/%.fasta/.fa}"done

for i in chr*do  NEWNAME="${i/%.fasta/.fa}"  mv -- "$i" "$NEWNAME"done

The "%{var/%pat/replacement}" looks for pat only at the end of the variable and replaces it with replacement.

bash for-loop batch-rename

for f in chr*.fasta; do mv "$f" "${f/%.fasta/.fa}"; done

bash for-loop batch-rename

If you have the rename command, you can do:

rename .fasta .fa chr*.fasta

CodeHunter