investigate meme file issue with java 07-16-2014d0916

2014-08-29

For some reason when I call glam2 with a system command from java, the meme file is not created properly.  The meme file is created properly when calling glam2 from the command prompt.  Why is this?

Here is an example of a command called in java that produces output, but not a meme file:
C:\cygwin\home\kurtw_000\meme\bin\glam2 -o "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-16-2014d0931\glam2test\glam2" p "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-16-2014d0931\glam2test\temp_collection_of_good_motifs.fa" -n 1000 -a 2 -r 2

If I call this command from the command line,
C:\cygwin\home\kurtw_000\meme\bin\glam2 -o "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-16-2014d0931\glam2test\glam2" p "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-16-2014d0931\glam2test\temp_collection_of_good_motifs.fa" -n 1000 -a 2 -r 2
then I also do not get a meme file.

If I call this command,
glam2 -o "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-16-2014d0931\glam2test\glam2" p "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-16-2014d0931\glam2test\temp_collection_of_good_motifs.fa" -n 1000 -a 2 -r 2
I also do not get a meme file

If I first change the directory, 
cd C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-16-2014d0931\glam2test
and then call the command
glam2 -o glam2 p temp_collection_of_good_motifs.fa -n 1000 -a 2 -r 2
then I do get the meme file

Can I change the directory in java?
Actually, I am already specifying the directory.

What if I just call
glam2 -o glam2 p temp_collection_of_good_motifs.fa -n 1000 -a 2 -r 2
in the appropriate directory in java?
It works!  I get the meme file

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