Hi zajtat,
If combining.executable infile1 infile2 > outfile1 produces the output you said it does, then running the command:

Code:

combining.executable infile3 outfile1 > outfile2

won't give you the output you said you want (it would put the data from infile3 before the data from end of the infile2 in outfile2 discarding everything from infile1, wouldn't it); wouldn't you need to use:

Code:

combining.executable outfile1 infile3 > outfile2

instead???

Do all of the ~6000 text files you want to combine have names that end in .txt (or some other single filename extension)? Are there any other files in that directory that have names that end in the same filename extension? If the 1st answer is yes and the 2nd answer is no, why do you need master-infile? Why not just use for i in *.txt? And, no, you don't want nested loops for this. What you have shown us in post #1 will combine two copies of infile1 into a files named 1 through 6000, and then for each of your other input files overwrite each of those numbered files with a combination of two copies of the next file in master-infile keeping only the 6000 copies of the combination of two copies of the last input file named in master-infile.

Is my interpretation of the commands you need to run correct? If not, please explain more clearly what arguments you are trying to pass to the command combining.executable.

Do you really want to keep outfile1 through outfile6000, or do you just want one outfile to be the combination of the 6000 input files? (Putting 12000 files in a single directory is usually a great way to slow down processing any files in that directory.)

Are you always processing exactly 6000 files, or do you just want to combine all of your text files (either based on a filename matching pattern or on the list of files in master-infile) no matter whether than is two files or a thousand files?

What is the format of the real names of your input files?

What name do you really want for your output file(s)?