Make the MUMMER4 runs into a .sh executable about vcfgenerator

[Critic-ism]

Unzipped gz file, renamed .fna to .fasta--remember to write directory so that the rename doesn't move the file to current directory. Test file is currently in intern2 personal directory with no permissions to move it back to ShewanellaAssmeblies. intern2 needs permissions to move files back into ShewanellaAssemblies

[ginaah]

Mummerplot command using -c -x "[0,1000000]" -y "[0,5000000]" -png -p mummer mummer2.mums not developing dot plot showing Maximal Unique Matches (MUM). Changing axis variables renders plot shown as pictured:

[Critic-ism]

Solved the issue with the visualization! Lowballed the x and y axis, x and y axis should be at LEAST equal to the genome length of Shewanella. Deleting the files and working on a loop for the mummer commands. Will make sure to write a portion of code to rename each mummer.png incrementally so it does not continue to overwrite each other.

[Critic-ism]

Script for unzipping .gz files and renaming .fna to .fasta files has been written. Writing permissions for ShewanellaAssemblies directory has also been given so mummer commands may be run with the files from that directory

[Critic-ism]

Conversion to png file does not show a working plot, but outputting it as a postscript (.ps) file shows a plot similar to what we should be seeing, retrying with another file and outputting as a postscript file to see if the issue is mummer or the visualization

[Critic-ism]

Trying to replicate the workflow did not work--postscript files do not show a proper visualization

[Critic-ism]

Redoing the practice mummer tutorial outputted the correct .ps file visualization--issue on our workflow may be related to the query files and reference file.

[Critic-ism]

Mummer scripts are completed and ran on both the test directory and the original directory. Scripts are written specifically for the VM directories so any future automation/editing will require tweaking to change directories and reference files.

[Critic-ism]

Mummer4 runs are working for the Shewanella project! Dot plots are in the drive.