i have already tried closing the file before calling the fasta34.exe..

-o $compare -Q $querry $library are for avoiding command line which other wise feed manually, ....if i remove the -Q $querry $library the program runs fine and i have to give the file name manually but the program hangs up further ...indicating use of uninitialize value at concatination

at if(m/>>(.{4,6})(.*)/)

under while (compare)

thanks