My script was just using two output files named 0
and 1 instead of 5,426 output files named ./result/1 through ./result/5246. For the sequence of commands shown above that your script produces, my script would have created the commands:

Code:

./match.pl  -f 9464294024_R01C01header -g 9466656017_R01C01header -k 1 -l 1 -v "5 6 7" > 0
./match.pl  -f 9464294024_R01C02header -g 0 -k 1 -l 1 -v "5 6 7" > 1
./match.pl  -f 9464294024_R02C01header -g 1 -k 1 -l 1 -v "5 6 7" > 0
./match.pl  -f 9464294024_R02C02header -g 0 -k 1 -l 1 -v "5 6 7" > 1
./match.pl  -f 9464294024_R03C01header -g 1 -k 1 -l 1 -v "5 6 7" > 0
./match.pl  -f 9464294024_R03C02header -g 0 -k 1 -l 1 -v "5 6 7" > 1
./match.pl  -f 9464294024_R04C01header -g 1 -k 1 -l 1 -v "5 6 7" > 0
./match.pl  -f 9464294024_R04C02header -g 0 -k 1 -l 1 -v "5 6 7" > 1
./match.pl  -f 9464294024_R05C01header -g 1 -k 1 -l 1 -v "5 6 7" > 0
./match.pl  -f 9464294024_R05C02header -g 0 -k 1 -l 1 -v "5 6 7" > 1

and the trace output log you showed us said that the line shown in red above failed with the diagnostic message:

Code:

Must specify file one using -g switch

What output do you get when you run the first three of the above sequence of commands manually?

The commands in your script are logically equivalent to the commands my script was trying to run, but didn't need the extra disk space for 5,245 temporary files that your script produces. If all 5,247 of the commands like those above had succeeded, my script would have then moved the last temporary output file (either 0 or 1) to a file named outfile and then would have removed the other temporary file.

I certainly don't claim that all of the code I produce is perfect. But the trace output you showed us from running my script (as you modified it to run your perl script) shows that commands like those shown above were being run and that the command shown in red above failed when there doesn't seem to be any reason that you have explained to us why it should not succeed. My belief is that there is something about the filename 0 that match.pl doesn't like, but without understanding why it doesn't like it (and what other filenames it doesn't like), I don't know how complex I need to make the trivial code that switches between files 0 and 1 to produce filenames that will be accepted.

Just saying that my code doesn't work doesn't help me help you. Showing us the contents of match.pl or telling us the restrictions match.pl places on -g option option-argument values would help us help you. We want to help you.