Because 'nohup' expects a single-word command and its arguments - not a shell loop construct. You'd have to use:
nohup sh -c 'for i in mydir/*.fasta; do ./myscript.sh "$i"; done >output.txt' &
You can do it on one line, but you might want to do it tomorrow too.
$ cat loopy.sh #!/bin/sh# a line of text describing what this task doesfor i in mydir/*.fast ; do ./myscript.sh "$i"done > output.txt$ chmod +x loopy.sh$ nohup loopy.sh &
For me, Jonathan's solution does not redirect correctly to output.txt. This one works better:
nohup bash -c 'for i in mydir/*.fasta; do ./myscript.sh "$i"; done' > output.txt &