The previous answers are all correct and you should be able to solve your problem with their aid.

Anyhow, i would like to address another topic of your question. Is there a specific reason you want to use velvet? What organisms do you intend to assemble? Do you know that velvet's performance highly depends on the k-mer parameter and, if velvet shall really be used, at least it's recommended to use VelvetOptimizer? By now, there have been several genome assembler evaluations and benchmarks which all show that velvet often is not the optimal choice (to put it diplomatically).

I'm not a big fan of advertising specific publications in user comments - especially not if those advertisement is for the own benefit - but i really feel that at least i should point to some of those studies here, which are: Assemblathon, Assemblathon 2, GAGE, GAGE-B, and very recently GABenchToB (that's mine, apologizes).

can you try to specify the location of the command you are using? like

a/b/c/subset_fastq.pl -i -o

Command not found means either the command does not physically exist in your harddrive or the Terminal doesn't know where it is

And since you are using OSX.6.8, your Xcode and Perl may not be the latest. Try to update them if you can. 

Also you can contact people in velvet for troubleshooting

good luck

I also agree with the first point Fang mentioned.  To execute subset_fastq.pl from command line you need it to be available in the bin directory from where default commands execute.  I don't think it is a problem of Mac OS or the software.  If you want to run any program which is not inside bin,  you should mention the full path of the program also you have to make sure that execution permission is given to the program.

Hope these will help.

Good luck.

I think that your problem does not come from the script itself but on how you try to execute it. Please take a look at, http://www.cyberciti.biz/faq/howto-run-a-script-in-linux/, for instance

Try to locate your perl script:

find / -name "yourscriptname.pl" 

os X finder can do a good job too.

then use full path

> perl /path/to/script/script.pl args

voilà ! 

As said before, you can't execute a command if the program is not in a directory included in the PATH variable.

>echo $PATH

will show you these directory. (usually ~/bin/ is there). if you want, you can store your script in ~/bin/ to access it from anywhere, or you can add the directory in the PATH variable. 

> export PATH=/the/path/tothe/script/:$PATH

this command has to be in a dotfile like .bashrc or .login on mac os X  so it's executed each time you open a terminal.

The previous answers are all correct and you should be able to solve your problem with their aid.

Anyhow, i would like to address another topic of your question. Is there a specific reason you want to use velvet? What organisms do you intend to assemble? Do you know that velvet's performance highly depends on the k-mer parameter and, if velvet shall really be used, at least it's recommended to use VelvetOptimizer? By now, there have been several genome assembler evaluations and benchmarks which all show that velvet often is not the optimal choice (to put it diplomatically).

I'm not a big fan of advertising specific publications in user comments - especially not if those advertisement is for the own benefit - but i really feel that at least i should point to some of those studies here, which are: Assemblathon, Assemblathon 2, GAGE, GAGE-B, and very recently GABenchToB (that's mine, apologizes).