Hi,

Each time you want to save an output from terminal to a file you can use the symbol > at the end of the command, with the name of your file.

​my_command > my_file

Or if you want to append content:

​my_command >> my_file

In MacOs for example, you can save the terminal content in a file with "command + S".

I do not know if it's exactly what you want, but if you run on multiples files, you just have to use a variable and change the file name automatically.

A simple loop to deal with all files than end with *.fasta in a dir:

for f in *.fasta; 
do 
NAME=$(basename "$f" .fasta); 
mkdir $NAME; 
prodigal -i $f -a $NAME/$NAME.faa -d $NAME/$NAME.ffn -o $NAME/$NAME.gff -f gff; 
done

You can delete the linebreaks and run the command as such.

A routine to run the same command/program for all the files of your current directory, generating a new folder and storing the results in it could be:

    for fil in `ls *.your_extension`;
    do
      filetag=`echo "$fil" | cut -d'.' -f1`;
      mkdir $filetag;
      your_program $fil > ./$filetag/output.your_extension;
    done

With this you read all the files with your selected extension in the working directory, generate a new folder there containing a base name generated from the original file name but without the extension and run your command/program storing the output to a file placed in it.