oligoMatch error

[tgeorgom]

Dear team ucsc,

I am trying to use your oligoMatch program in ubuntux64 environment. I downloaded the appropriate file from the server, I used as a test chrM.fa from the ucsc servers "goldenpath", in fasta format
and I made a fasta formated file that contains the sequence I want to interrogate.

file: apoi.fa
>apoi

RAATTY

the program gives me an output of

./oligoMatch apoi.fa chrM.fa
oligoMatch - find perfect matches in sequence.
usage:
oligoMatch oligos sequence output.bed
where "oligos" and "sequence" can be .fa, .nib, or .2bit files.
The oligos may contain IUPAC codes.

Do you have any clue of what I am missing or what I am doing wrong?

Kindest Regards
Theodoros Georgomanolis

-- 
Dr Theodoros Georgomanolis,
Zentrum für Molekulare Medizin (ZMMK)
Universität zu Köln
ZMMK-Forschungsgebäude
Geb. 66 Raum 1.033
Robert-Koch-Str. 21
D-50931 Köln
Germany
tel (+49)0221 478-89598 

[Hiram Clawson]

Good Morning Theodoros:

Please supply a third argument to the program, the 'output.bed'
file to receive the results of the analysis:

./oligoMatch apoi.fa chrM.fa apoi.bed

The 'usage:' statement indicates the required arguments.
You can also use the argument 'stdout' in place of 'apoi.bed'
to see the output going to 'standard output'
https://en.wikipedia.org/wiki/Standard_streams#Standard_output_.28stdout.29

--Hiram