sffinfo from perl script not working

Commands in mothur
1

Hello,
I am not sure if this is the right place to post my question, so I apologize if it really isn´t, maybe it is more perl question, but I´ll still ask :).

I am beginner in programming and I´ve just started to analyze my first 454 dataset. It consists of cca 40 sff files (one for each primer pair, that´s how I got them from the seq guys).

I didn´t find an option to use sffinfo recursively within mothur, so I wanted to write a perl script calling mothur.

I decided to try with a single file first.

When I run my script, mothur opens, starts extracting and then I get:

[ERROR]: Could not open /Users/microbiome1/HCL7W1A02.TMID1.fasta
[ERROR]: Could not open /Users/microbiome1/HCL7W1A02.TMID1.qual
[ERROR]: Could not open /Users/microbiome1/HCL7W1A02.TMID1.flow
3689
It took 0 secs to extract 3689.
Output File Names:
/Users/microbiome1/HCL7W1A02.TMID1.fasta
/Users/HCL7W1A02.TMID1.qual
/Users/microbiome1/HCL7W1A02.TMID1.flow

And mothur quits.

Does anyone have idea what went wrong? I´d be grateful for any response or hints.
Thanks.

2

It seems like mothur can’t open the output files. Do you have write permissions on the /Users/microbiome1/ folder?

3

I can´t believe I haven´t notice that. Forgot to switch to superuser.
Thanks for pointing that out. It probably saved me a lot of time.