This repo works fine, it's for an update that's not online yet. I would like to send code to clarify, but I thought it would distract the attention from the real problem, because i tried many types of system calls, all fail when the hash takes up a lot of memory. That is the only connection I find, I really don't understand the problem, it's the first time I am this stuck, that's why I asked this question.

I got this error now: 'Cannot allocate memory', Don't know why I didn't saw this before. So I guess a system call needs to copy the complete virtual memory to the sister process.

So I guess I can not use system calls, I wil try if I have the same problem with Backticks.. If you would know other alternatives, I would always happy to hear it.

This is the system call I would eventually need:

system('blastn -query '.$output_file1.' -subject '.$ref_file.' -out BLAST_tmp.txt -outfmt 10')