/projects/compbio/experiments/models.97/scripts/quick-condor "predict-2nd < 
./run-scripts/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.script
> & dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.log" &

First test with running the condor cluster:

[oink:burial> /projects/compbio/experiments/models.97/scripts/quick-condor "predict-2nd < 
dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.script >& 
dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.log" &

Log File Location: /projects/compbio2/usr/karplus/predict-2nd/testing/burial/
	dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.log
Output stored in log file:
# command:# Read 5 alphabets from /projects/compbio/lib/alphabet/two-spot-burial.alphabet
# command:# Prefix for input files set to /cse/faculty/karplus/dna/predict-2nd/testing/
# command:# Prefix for output files set to /cse/faculty/karplus/dna/predict-2nd/testing/burial/
# command:NameToPtr::FindOldName expected to find name near_backbone_7 in the table of 21 names.

Analysis of predict-2nd:
The first big thing predict-2nd does is calls read_scripts on the provided script.
read_script is a command located in /projects/compbio/programs/ultimate/src/Command/
Command.h that just calls read_command which simply executes the next command to be
read from the script. This is where the "# command:" from in the begining of each line
of the log file.

Analysis of each command in the script file (dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.script):
Line 1: ReadAlphabet /projects/compbio/lib/alphabet/two-spot-burial.alphabet

ReadAlphabet function is called from ReadCommands.cc, in this function load_alphabet_file
is called (located in Alphabet.cc). load_alphabet_file in summary returns the number
of alphabets in an alphabet definition file. If you look at the alphabet file you see 
there are exactly 5 alphabets just as the log file states.

Line 2: InFilePrefix  /cse/faculty/karplus/dna/predict-2nd/testing/
	Same pattern as above but with InFilePrefix.
Line 3: OutFilePrefix /cse/faculty/karplus/dna/predict-2nd/testing/burial/
	Same pattern as above but with OutFilePrefix.

Line 4: ReadNeuralNet burial/networks/IDaaHr-5-15-7-15-9-15-13-near-backbone-7-empty.net

Again the same pattern as above is followed here, except I start to get lost
in the c++. In the end at some point there is NameToPtr::FindOldName call that has
ifnew variable set to ErrorIfNew. That results in the error message in the log file:
NameToPtr::FindOldName expected to find name near_backbone_7 in the table of 21 names.

The code starts with ReadNeuralNet in ReadCommands.cc and then gets confussing when it
calls NeuralNet::read_new(istream& in) in NeuralNet.cc.

Best thing to do is meet in person to discuss this.


PROBLEM SOLVED... near-backbone-7 net 1+2 completed.


3-2-04 Script runs started running in following order:

/projects/compbio/experiments/models.97/scripts/quick-condor "predict-2nd <

7 runs:

./run-scripts/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.script > & 
dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.log" &
DONE
./run-scripts/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-way-back-7-from-empty.script > & 
dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-way-back-7-from-empty.log" &
DONE-- RERUNNING

./run-scripts/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.script > & 
dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.log" &
DONE
./run-scripts/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-way-back-7-from-empty.script > & 
dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-way-back-7-from-empty.log" &
DONE-- RERUNNING 

./run-scripts/dunbrack-in-scop-2+3-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.script > & 
dunbrack-in-scop-2+3-IDaaHr-5-15-7-15-9-15-13-near-backbone-7-from-empty.log" &
DONE
./run-scripts/dunbrack-in-scop-2+3-IDaaHr-5-15-7-15-9-15-13-way-back-7-from-empty.script > & 
dunbrack-in-scop-2+3-IDaaHr-5-15-7-15-9-15-13-way-back-7-from-empty.log" &
DONE-- STILL NEEDS TO BE RERUN

./run-scripts/t2k-5631-5-15-7-15-9-15-13-near-backbone-7-from-empty.script >& 
./t2k-5631-5-15-7-15-9-15-13-near-backbone-7-from-empty.log" &
DONE
./run-scripts/t2k-5631-5-15-7-15-9-15-13-way-back-7-from-empty.script >& 
./t2k-5631-5-15-7-15-9-15-13-way-back-7-from-empty.log" &
RUNNING bark, should be RERUN
11 runs:

./run-scripts/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-11-from-empty.script > & 
dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-near-backbone-11-from-empty.log" &
RUN SCRIPT DOES NOT EXIST
./run-scripts/dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-way-back-11-from-empty.script > & 
dunbrack-in-scop-1+2-IDaaHr-5-15-7-15-9-15-13-way-back-11-from-empty.log" &
ERROR with incosistant number of interfaces and neural layers

./run-scripts/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-near-backbone-11-from-empty.script > & 
dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-near-backbone-11-from-empty.log" &
RUN SCRIPT DOES NOT EXIST
./run-scripts/dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-way-back-11-from-empty.script > & 
dunbrack-in-scop-1+3-IDaaHr-5-15-7-15-9-15-13-way-back-11-from-empty.log" &


./run-scripts/dunbrack-in-scop-2+3-IDaaHr-5-15-7-15-9-15-13-near-backbone-11-from-empty.script > & 
dunbrack-in-scop-2+3-IDaaHr-5-15-7-15-9-15-13-near-backbone-11-from-empty.log" &
RUN SCRIPT DOES NOT EXIST
./run-scripts/dunbrack-in-scop-2+3-IDaaHr-5-15-7-15-9-15-13-way-back-11-from-empty.script > & 
dunbrack-in-scop-2+3-IDaaHr-5-15-7-15-9-15-13-way-back-11-from-empty.log" &


./run-scripts/t2k-5631-5-15-7-15-9-15-13-near-backbone-11-from-empty.script >&
./t2k-5631-5-15-7-15-9-15-13-near-backbone-11-from-empty.log" &

./run-scripts/t2k-5631-5-15-7-15-9-15-13-way-back-11-from-empty.script >&
./t2k-5631-5-15-7-15-9-15-13-way-back-11-from-empty.log" &