p = 0.0001 pairwise RLS difference in biogrid PPI

10K permutation test
10:05am start at ridgeside, 8 core run. Expect 3 hour run.

(in progress) PBS run 1.ori.ginppi.2015Oct

/home/hongqin/temp_project/mactower-network-failure-simulation/1.ori.ginppi.2015Oct

[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ cat ori_aging_loopgordon.pbs 

#!/bin/bash

#PBS -l nodes=1:ppn=16

#PBS -l walltime=07:00:00:00

module load R

echo hostname

cd /oasis/scratch/hongqin/temp_project/mactower-network-failure-simulation/1.ori.ginppi.2015Oct

pwd

for p in 1.0 0.99 0.98 0.97 0.96 0.95 0.94 0.93 0.92 0.91 0.9 0.89 0.88 0.87 0.86 0.85 0.82 0.8 

do

   #for LOne in 0.002 0.0021 0.0022 0.0023 0.0024 0.0025 0.0026 0.0028 0.0028 0.0029 0.003 0.0035 0.004 0.0045

   for LOne in 0.001 0.0011 0.0012 0.0013 0.0014 0.0015 00016 0.0017 0.0018 0.0019 0.002

   do

      echo "$p $LOne"

 Rscript netwk_aging_sim.v0.1b.R -if1 merged_PPIGIN_Factorized2015Oct132Cols.csv -if2 essentialGeneLookupTable_20151013.csv -l1 $LOne -l2 0 -dt 4 -p $p -n 5000 -op ginppi -od ginppi.ori.out -iC 16 -d 1 -h /oasis/scratch/hongqin/temp_project/mactower-network-failure-simulation/1.ori.ginppi.2015Oct

   done

done

[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ qstat -u hongqin

gordon-fe2.local: 

                                                                                  Req'd    Req'd       Elap

Job ID                  Username    Queue    Jobname          SessID  NDS   TSK   Memory   Time    S   Time

----------------------- ----------- -------- ---------------- ------ ----- ------ ------ --------- - ---------

2394355.gordon-fe2.loc  hongqin     normal   ori_aging_loopgo 113139     1     16    --  168:00:00 R  00:10:54

Job started at 10:30am --> 

[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ cat ori_aging_loopgordon.2.pbs 

#!/bin/bash

#PBS -l nodes=1:ppn=16

#PBS -l walltime=07:00:00:00

module load R

echo hostname

cd /oasis/scratch/hongqin/temp_project/mactower-network-failure-simulation/1.ori.ginppi.2015Oct

pwd

for p in 1.0 0.99 0.98 0.97 0.96 0.95 0.94 0.93 0.92 0.91 0.9 0.89 0.88 0.87 0.86 0.85 0.82 0.8 

do

   for LOne in 0.001 0.0011 0.0012 0.0013 0.0014 0.0015 00016 0.0017 0.0018 0.0019 0.002 0.0021 0.0022 0.0023 0.0024 0.0025 0.0026 0.0028 0.0028 0.0029 0.003 0.0035 0.004 0.0045

   do

      echo "$p $LOne"

 Rscript netwk_aging_sim.v0.1b.R -if1 merged_PPIGIN_Factorized2015Oct132Cols.csv -if2 essentialGeneLookupTable_20151013.csv -l1 $LOne -l2 0 -dt 5 -p $p -n 2500 -op ginppi -od ginppi.ori.out -iC 16 -d 1 -h /oasis/scratch/hongqin/temp_project/mactower-network-failure-simulation/1.ori.ginppi.2015Oct

   done

done

[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ qstat -u hongqin

gordon-fe2.local: 

                                                                                  Req'd    Req'd       Elap

Job ID                  Username    Queue    Jobname          SessID  NDS   TSK   Memory   Time    S   Time

----------------------- ----------- -------- ---------------- ------ ----- ------ ------ --------- - ---------

2394355.gordon-fe2.loc  hongqin     normal   ori_aging_loopgo 113139     1     16    --  168:00:00 R  00:19:15

2394382.gordon-fe2.loc  hongqin     normal   ori_aging_loopgo 103945     1     16    --  168:00:00 R  00:01:09

* Network aging simulation batch run on Mactower, (in progress)

After 12-8 weekend power shutdown, I re-started the run in two parallel job in bash. (Parallel jobs are confusing to run in Rstudio because the screen show results of both jobs. )

job1: 

helen:ms02GINPPI hqin$ nohup R -f net-aging-sim-2014Feb24.R 

appending output to nohup.out

job2: 

helen:ms02GINPPI hqin$ nohup R -f net-aging-sim-2014Feb24-run2.R &

[1] 464

helen:ms02GINPPI hqin$ appending output to nohup.out

Power turned off during the winter break.

Rerun the two jobs on Jan 9, 2015