/ Bio Informatics

running pace new method

Step 1. generate datafile with n sequences

head -n*2 original.fsa > small_sample.fsa

Step 2. run preprocess

./preprocessPaCE 5k.fsa 1

Step 3. run GItitle.pl

./GItitle.pl 5k.fsa.PaCE > 5k.GI.fsa

Step 4. run PaCE

!/bin/csh

@ job_type = parallel

@ class = LONG

@ account_no = NONE

@ node = 2

@ tasks_per_node = 4

@ checkpoint = no

@ wall_clock_limit = 05:00:00

@ error = $(Executable).$(Cluster).err

@ output = $(Executable).$(Cluster).out

@ environment = COPY_ALL

@ queue

llmachinelist
mpirun -v -np 8 -machinefile /tmp/machinelist.$LOADL_STEP_ID ./PaCE_v9
/N/gpfs/cap3/leesangm/HumanMRNA/split1mil/5k.GI.PaCE 5000
./Phase.cfg

llsubmit submitTest.sh

Step 5. split PaCE output

./PaCEclusterFasta.pl test.fsa estClust.5000.3.PaCE

Notes

1. Pace: How to run

mpirun -v -np 8 ./PaCE /N/gpfs/cap3/leesangm/HumanMRNA/example5K/5k.GI.fsa 5000 ./PaCE.cfg

Prashanth Madi

Prashanth Madi

I'm a programmer & Tech enthusiast. I work for OpenSource Support Team at Microsoft, but this blog, its content & opinions are my own. I blog about tech, gadgets, code, where we're going & we've been.

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