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To use scp you will need to open a second terminal window that is on your desktop and not on the remote TACC system. It can be tricky to figure out where the files are on the remote TACC system, because your desktop won't understand what $HOME, $WORK, $SCRATCH mean (they are only defined on TACC).

To figure out the full path to your file, you can use the pwd command in your terminal on TACC in the window that you ran breseq in (it should contain an "output" folder). Rather than copying the entire contents of the folder which can be rather large, we are going to add a twist of compressing the entire folder into a single compressed archive using the tar command so that the size will be smaller and it will transfer faster:

cd $SCRATCH/BDIB_breseq_lambda_mixed_pop
tar -czvf output.tar.gz output  # the czvf options in order mean Create, Zip, Verbose, Force
pwd

Then you can then copy paste that information (in the correct position) into the scp command on the desktop's command line:

scp -r <username>@ls5.tacc.utexas.edu:<the_directory_returned_by_pwd>/output.tar.gz .
 
# Enter your password and Token number and wait for the file transfer to complete
 
tar -xvzf output.tar.gz  # the new "x" option at the front means eXtract