WindowMasker

WindowMasker is a denovo repeat finder from the NCBI, published in 2006.

UCSC Installation

It was taken from the NCBI C++ Toolkit (Dec. 2005) and installed into

/cluster/bin/x86_64

the following way:

ssh kolossus
cd /scratch/andy
wget ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/CURRENT/ncbi_cxx--Dec_31_2005.tar.gz
tar xfz ncbi_cxx--Dec_31_2005.tar.gz 
cd ncbi_cxx--Dec_31_2005
./configure --without-debug --with-optimization --with-projects=src/app/winmasker/windowmasker.lst
cd /scratch/andy/ncbi_cxx--Dec_31_2005/GCC344-Release64/build && make all_p
cd app/winmasker/
cp windowmasker /cluster/bin/x86_64/

The README file in src/app/winmasker looks enough like a man file so

cd /scratch/andy/ncbi_cxx--Dec_31_2005/src/app/winmasker
cp README /cluster/bin/man/man1/winmasker.1

Opossum Experiment

• Running chr8 on hgwdev64 took about 5 min. Not bad.
• Trying this thing genome-wide was a problem. It was never using more than 2 gigs of RAM and after about 2.5 hours it errored.
• Running on the pitakluster was a problem too. Apparently this program communicates with the NCBI over the internet. Seems a little suspicious.
• The results of the one-chromosome-at-a-time run on kolossus:

real    228m34.868s
user    72m38.388s
sys     15m1.872s