EMP Biom Files Pt. VI - Green Planet

Got access to the Green Planet server and am able to login.

Was informed by Chad Cantwell that QIIME may or may not be installed in the new environment (server was updated recently and it may not be running)

Contacted  Steve Hatosy (from Adam's lab) and was super helpful.
When you login to the server (through ssh), type: . /sopt/qiime/set_paths_1.4
This should set the paths to the QIIME script

Code to run:
split_otu_table_by_taxonomy.py
-i full_emp_table_w_tax.biom #open source biom file
-L 5 #split taxonomy at Family level
-o ./L5/ #file directory

>> SystemError: Negative size passed to PyString_FromStringAndSize

This is (I think) due to large size of the input file (biom file 2.63 GB). From my correspondence with people in the Knight Lab, the file should need ~30GB of memory to load.

Protocol for Cluster:

1. ssh -Y abchase@gplogin3.ps.uci.edu
2. enter login information
3. pwd #gets cluster directory 
4. exit cluster
5. from local terminal. you can upload files to the cluster:
1. scp /Users/MartinyLab/Desktop/alexs-stuff/EMP/EMPopen/full_emp_table_w_tax.biom abchase@gplogin1.ps.uci.edu:/home/abchase
6. Run QIIME code with cluster file directory