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WindowMasker is a denovo repeat finder from the NCBI, published in 2006.
It was taken from the NCBI C++ Toolkit (Dec. 2005) and installed into
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
- 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