Goal

Accuracy as a function of isotope incorporation & community similarity among replicate microcosms

Variable parameters:

  • shared % of taxa
    • 80, 85, 90, 95, 100
  • permuted % of rank abundances
    • 20, 15, 10, 5, 0
  • atom % isotope incorporation
    • 50
  • % taxa that incorporate
    • 10
  • n-reps (stocastic: taxon abundances & which incorporate)
    • 10

Setting paths


In [1]:
# paths
import os

workDir = '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/'
buildDir = os.path.join(workDir, 'microBetaDiv')
R_dir = '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/SIPSimR/scripts/'

fragFile = '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/ampFrags_kde.pkl'
genome_index = '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/genome_index.txt'

Init


In [2]:
import glob
import itertools
import nestly

In [3]:
%load_ext pushmsg

In [4]:
if not os.path.isdir(buildDir):
    os.makedirs(buildDir)
%cd $buildDir


/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv

BD min/max


In [5]:
## min G+C cutoff
min_GC = 13.5
## max G+C cutoff
max_GC = 80
## max G+C shift
max_13C_shift_in_BD = 0.036


min_BD = min_GC/100.0 * 0.098 + 1.66    
max_BD = max_GC/100.0 * 0.098 + 1.66    

max_BD = max_BD + max_13C_shift_in_BD

print('Min BD: {}'.format(min_BD))
print('Max BD: {}'.format(max_BD))


Min BD: 1.67323
Max BD: 1.7744

Nestly


In [7]:
# making an experimental design file for qSIP
x = range(1,7)
y = ['control', 'treatment']

expDesignFile = os.path.join(buildDir, 'qSIP_exp_design.txt')
with open(expDesignFile, 'wb') as outFH:
    for i,z in itertools.izip(x,itertools.cycle(y)):
        line = '\t'.join([str(i),z])
        outFH.write(line + '\n')

!head $expDesignFile


1	control
2	treatment
3	control
4	treatment
5	control
6	treatment

Nestly params


In [8]:
# building tree structure
nest = nestly.Nest()


# varying params
nest.add('shared_perc', [80, 85, 90, 95, 100])
nest.add('perm_perc', [0, 5, 10, 15, 20])
nest.add('rep', range(1,11))

## set params
nest.add('percIncorp', [50], create_dir=False)
nest.add('percTaxa', [10], create_dir=False)
nest.add('abs', ['1e9'], create_dir=False)
#nest.add('abs', ['1e7'], create_dir=False)           # TEST
nest.add('np', [10], create_dir=False)
nest.add('Monte_rep', [100000], create_dir=False)
nest.add('subsample_dist', ['lognormal'], create_dir=False)
nest.add('subsample_mean', [9.432], create_dir=False)
nest.add('subsample_scale', [0.5], create_dir=False)
nest.add('subsample_min', [10000], create_dir=False)
nest.add('subsample_max', [30000], create_dir=False)
nest.add('min_BD', [min_BD], create_dir=False)
nest.add('max_BD', [max_BD], create_dir=False)
nest.add('DBL_scaling', [0.5], create_dir=False)
nest.add('bandwidth', [0.8], create_dir=False)
nest.add('heavy_BD_min', [1.71], create_dir=False)
nest.add('heavy_BD_max', [1.75], create_dir=False)
nest.add('topTaxaToPlot', [100], create_dir=False)
nest.add('padj', [0.1], create_dir=False)
nest.add('log2', [0.25], create_dir=False)

### input/output files
nest.add('buildDir', [buildDir], create_dir=False)
nest.add('R_dir', [R_dir], create_dir=False)
nest.add('genome_index', [genome_index], create_dir=False)
nest.add('fragFile', [fragFile], create_dir=False)
nest.add('exp_design', [expDesignFile], create_dir=False)


# building directory tree
nest.build(buildDir)

# bash file to run
bashFile = os.path.join(buildDir, 'SIPSimRun.sh')

Experimental design


In [9]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_expDesign.sh'
bashFileTmp


Out[9]:
'/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/SIPSimRun_expDesign.sh'

In [10]:
%%writefile $bashFileTmp
#!/bin/bash
source activate SIPSim
# OPENBLAS threads 
export OMP_NUM_THREADS=1

echo '#-- Experimental design --#'

echo '# Making an isotope incorporation config file'
echo '## 3 replicate gradients for control & treatment'
SIPSim incorp_config_example \
  --percIncorpUnif {percIncorp} \
  --n_reps 3 \
  > incorp.config

echo '# Selecting incorporator taxa'
echo '## This is to make the gradient replicates consistent (qSIP finds mean among replicates)'
SIPSim KDE_select_taxa \
    -p {percTaxa} \
    {fragFile} \
    > incorporators.txt

echo '# Creating a community file (3 replicate control, 3 replicate treatment)'
SIPSim communities \
    --richness 950 \
    --config incorp.config \
    --shared_perc {shared_perc} \
    --perm_perc {perm_perc} \
    {genome_index} \
    > comm.txt       

echo '# simulating gradient fractions'
SIPSim gradient_fractions \
    --BD_min {min_BD} \
    --BD_max {max_BD} \
    comm.txt \
    > fracs.txt


Writing /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/SIPSimRun_expDesign.sh

In [11]:
!chmod 755 $bashFileTmp

In [12]:
%%bash -s $workDir $bashFileTmp $buildDir
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate py2_ley0.4
# change to working dir
cd $1
# run job 
nestrun --template-file $2 -d $3 --log-file exp_design.log -j 20


2017-08-18 08:23:46,829 * INFO * Template: ./SIPSimRun_expDesign.sh
2017-08-18 08:23:46,834 * INFO * [15095] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/1
2017-08-18 08:23:46,838 * INFO * [15097] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/2
2017-08-18 08:23:46,842 * INFO * [15105] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/3
2017-08-18 08:23:46,847 * INFO * [15114] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/4
2017-08-18 08:23:46,851 * INFO * [15122] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/5
2017-08-18 08:23:46,857 * INFO * [15130] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/6
2017-08-18 08:23:46,861 * INFO * [15138] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/7
2017-08-18 08:23:46,866 * INFO * [15146] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/8
2017-08-18 08:23:46,870 * INFO * [15154] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/9
2017-08-18 08:23:46,875 * INFO * [15162] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/10
2017-08-18 08:23:46,880 * INFO * [15170] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/1
2017-08-18 08:23:46,884 * INFO * [15179] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/2
2017-08-18 08:23:46,890 * INFO * [15188] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/3
2017-08-18 08:23:46,895 * INFO * [15195] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/4
2017-08-18 08:23:46,901 * INFO * [15204] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/5
2017-08-18 08:23:46,908 * INFO * [15212] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/6
2017-08-18 08:23:46,913 * INFO * [15220] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/7
2017-08-18 08:23:46,919 * INFO * [15228] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/8
2017-08-18 08:23:46,924 * INFO * [15234] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/9
2017-08-18 08:23:46,930 * INFO * [15244] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/10
2017-08-18 08:24:00,283 * INFO * [15130] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/6 Finished with 0
2017-08-18 08:24:00,290 * INFO * [15875] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/1
2017-08-18 08:24:00,324 * INFO * [15138] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/7 Finished with 0
2017-08-18 08:24:00,329 * INFO * [15883] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/2
2017-08-18 08:24:00,330 * INFO * [15220] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/7 Finished with 0
2017-08-18 08:24:00,337 * INFO * [15888] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/3
2017-08-18 08:24:00,367 * INFO * [15114] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/4 Finished with 0
2017-08-18 08:24:00,381 * INFO * [15899] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/4
2017-08-18 08:24:00,404 * INFO * [15146] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/8 Finished with 0
2017-08-18 08:24:00,409 * INFO * [15907] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/5
2017-08-18 08:24:00,415 * INFO * [15204] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/5 Finished with 0
2017-08-18 08:24:00,420 * INFO * [15915] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/6
2017-08-18 08:24:00,444 * INFO * [15234] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/9 Finished with 0
2017-08-18 08:24:00,451 * INFO * [15923] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/7
2017-08-18 08:24:00,501 * INFO * [15170] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/1 Finished with 0
2017-08-18 08:24:00,507 * INFO * [15931] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/8
2017-08-18 08:24:00,508 * INFO * [15188] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/3 Finished with 0
2017-08-18 08:24:00,515 * INFO * [15934] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/9
2017-08-18 08:24:00,518 * INFO * [15162] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/10 Finished with 0
2017-08-18 08:24:00,536 * INFO * [15943] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/10
2017-08-18 08:24:00,572 * INFO * [15154] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/9 Finished with 0
2017-08-18 08:24:00,582 * INFO * [15955] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/1
2017-08-18 08:24:00,583 * INFO * [15097] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/2 Finished with 0
2017-08-18 08:24:00,590 * INFO * [15960] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/2
2017-08-18 08:24:00,591 * INFO * [15105] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/3 Finished with 0
2017-08-18 08:24:00,598 * INFO * [15968] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/3
2017-08-18 08:24:00,666 * INFO * [15195] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/4 Finished with 0
2017-08-18 08:24:00,680 * INFO * [15979] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/4
2017-08-18 08:24:00,680 * INFO * [15122] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/5 Finished with 0
2017-08-18 08:24:00,687 * INFO * [15982] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/5
2017-08-18 08:24:00,688 * INFO * [15212] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/6 Finished with 0
2017-08-18 08:24:00,694 * INFO * [15990] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/6
2017-08-18 08:24:00,694 * INFO * [15244] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/10 Finished with 0
2017-08-18 08:24:00,700 * INFO * [15998] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/7
2017-08-18 08:24:00,714 * INFO * [15228] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/8 Finished with 0
2017-08-18 08:24:00,720 * INFO * [16011] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/8
2017-08-18 08:24:00,720 * INFO * [15095] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/1 Finished with 0
2017-08-18 08:24:00,727 * INFO * [16018] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/9
2017-08-18 08:24:00,756 * INFO * [15179] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/2 Finished with 0
2017-08-18 08:24:00,761 * INFO * [16027] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/10
2017-08-18 08:24:11,877 * INFO * [15883] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/2 Finished with 0
2017-08-18 08:24:11,885 * INFO * [16658] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/1
2017-08-18 08:24:11,886 * INFO * [15943] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/10 Finished with 0
2017-08-18 08:24:11,890 * INFO * [16661] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/2
2017-08-18 08:24:11,922 * INFO * [15979] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/4 Finished with 0
2017-08-18 08:24:11,936 * INFO * [16674] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/3
2017-08-18 08:24:11,950 * INFO * [15960] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/2 Finished with 0
2017-08-18 08:24:11,955 * INFO * [16682] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/4
2017-08-18 08:24:11,969 * INFO * [15955] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/1 Finished with 0
2017-08-18 08:24:11,974 * INFO * [16690] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/5
2017-08-18 08:24:11,977 * INFO * [15998] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/7 Finished with 0
2017-08-18 08:24:11,983 * INFO * [16698] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/6
2017-08-18 08:24:11,983 * INFO * [15888] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/3 Finished with 0
2017-08-18 08:24:11,991 * INFO * [16703] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/7
2017-08-18 08:24:11,991 * INFO * [15915] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/6 Finished with 0
2017-08-18 08:24:11,999 * INFO * [16711] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/8
2017-08-18 08:24:12,000 * INFO * [15923] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/7 Finished with 0
2017-08-18 08:24:12,007 * INFO * [16722] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/9
2017-08-18 08:24:12,008 * INFO * [15934] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/9 Finished with 0
2017-08-18 08:24:12,022 * INFO * [16729] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/10
2017-08-18 08:24:12,022 * INFO * [15968] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/3 Finished with 0
2017-08-18 08:24:12,028 * INFO * [16733] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/1
2017-08-18 08:24:12,029 * INFO * [15990] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/6 Finished with 0
2017-08-18 08:24:12,037 * INFO * [16745] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/2
2017-08-18 08:24:12,044 * INFO * [15931] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/8 Finished with 0
2017-08-18 08:24:12,049 * INFO * [16751] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/3
2017-08-18 08:24:12,053 * INFO * [15982] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/5 Finished with 0
2017-08-18 08:24:12,064 * INFO * [16763] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/4
2017-08-18 08:24:12,069 * INFO * [16027] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/10 Finished with 0
2017-08-18 08:24:12,075 * INFO * [16773] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/5
2017-08-18 08:24:12,092 * INFO * [16018] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/9 Finished with 0
2017-08-18 08:24:12,098 * INFO * [16781] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/6
2017-08-18 08:24:12,128 * INFO * [15899] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/4 Finished with 0
2017-08-18 08:24:12,135 * INFO * [16789] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/7
2017-08-18 08:24:12,135 * INFO * [15875] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/1 Finished with 0
2017-08-18 08:24:12,139 * INFO * [16792] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/8
2017-08-18 08:24:12,185 * INFO * [15907] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/5 Finished with 0
2017-08-18 08:24:12,191 * INFO * [16805] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/9
2017-08-18 08:24:12,195 * INFO * [16011] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/8 Finished with 0
2017-08-18 08:24:12,200 * INFO * [16812] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/10
2017-08-18 08:24:22,053 * INFO * [16658] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/1 Finished with 0
2017-08-18 08:24:22,065 * INFO * [17444] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/1
2017-08-18 08:24:22,197 * INFO * [16698] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/6 Finished with 0
2017-08-18 08:24:22,204 * INFO * [17452] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/2
2017-08-18 08:24:22,215 * INFO * [16682] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/4 Finished with 0
2017-08-18 08:24:22,222 * INFO * [17460] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/3
2017-08-18 08:24:22,222 * INFO * [16729] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/10 Finished with 0
2017-08-18 08:24:22,229 * INFO * [17463] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/4
2017-08-18 08:24:22,283 * INFO * [16789] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/7 Finished with 0
2017-08-18 08:24:22,291 * INFO * [17476] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/5
2017-08-18 08:24:22,318 * INFO * [16674] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/3 Finished with 0
2017-08-18 08:24:22,325 * INFO * [17484] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/6
2017-08-18 08:24:22,325 * INFO * [16722] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/9 Finished with 0
2017-08-18 08:24:22,330 * INFO * [17487] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/7
2017-08-18 08:24:22,348 * INFO * [16773] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/5 Finished with 0
2017-08-18 08:24:22,360 * INFO * [17500] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/8
2017-08-18 08:24:22,400 * INFO * [16690] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/5 Finished with 0
2017-08-18 08:24:22,408 * INFO * [17508] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/9
2017-08-18 08:24:22,437 * INFO * [16661] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/2 Finished with 0
2017-08-18 08:24:22,442 * INFO * [17516] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/10
2017-08-18 08:24:22,462 * INFO * [16751] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/3 Finished with 0
2017-08-18 08:24:22,466 * INFO * [17524] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/10/1
2017-08-18 08:24:22,467 * INFO * [16733] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/1 Finished with 0
2017-08-18 08:24:22,472 * INFO * [17527] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/10/2
2017-08-18 08:24:22,472 * INFO * [16763] /ebio/abt3_projects/methano
limit_output extension: Maximum message size of 20000 exceeded with 79518 characters

In [13]:
%pushmsg "exp_design complete: $buildDir"

SIPSim pipeline


In [15]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_SIPSim-pipeline.sh'
bashFileTmp


Out[15]:
'/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/SIPSimRun_SIPSim-pipeline.sh'

In [16]:
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim
# OPENBLAS threads 
export OMP_NUM_THREADS=1


echo '#-- SIPSim pipeline --#'    
    
echo '# Adding diffusion'    
SIPSim diffusion \
    -n {Monte_rep} \
    --bw {bandwidth} \
    --np {np} \
    {fragFile} \
    > ampFrags_KDE_dif.pkl    

echo '# Adding DBL contamination; abundance-weighted smearing'
SIPSim DBL \
    -n {Monte_rep} \
    --comm comm.txt \
    --commx {DBL_scaling} \
    --np {np} \
    ampFrags_KDE_dif.pkl \
    > ampFrags_KDE_dif_DBL.pkl 

echo '# Adding isotope incorporation to BD distribution'
SIPSim isotope_incorp \
    -n {Monte_rep} \
    --comm comm.txt \
    --taxa incorporators.txt \
    --np {np} \
    ampFrags_KDE_dif_DBL.pkl \
    incorp.config \
    > ampFrags_KDE_dif_DBL_inc.pkl

echo '# Simulating an OTU table'
SIPSim OTU_table \
    --abs {abs} \
    --np {np} \
    ampFrags_KDE_dif_DBL_inc.pkl \
    comm.txt \
    fracs.txt \
    > OTU_abs{abs}.txt
    
echo '# Simulating PCR'
SIPSim OTU_PCR \
    OTU_abs{abs}.txt \
    > OTU_abs{abs}_PCR.txt    
    
echo '# Subsampling from the OTU table (simulating sequencing of the DNA pool)'
SIPSim OTU_subsample \
    --dist {subsample_dist} \
    --dist_params mean:{subsample_mean},sigma:{subsample_scale} \
    --min_size {subsample_min} \
    --max_size {subsample_max} \
    OTU_abs{abs}_PCR.txt \
    > OTU_abs{abs}_PCR_sub.txt
        
echo '# Making a wide-formatted table'
SIPSim OTU_wide_long -w \
    OTU_abs{abs}_PCR_sub.txt \
    > OTU_abs{abs}_PCR_sub_w.txt
    
echo '# Making metadata (phyloseq: sample_data)'
SIPSim OTU_sample_data \
    OTU_abs{abs}_PCR_sub.txt \
    > OTU_abs{abs}_PCR_sub_meta.txt
       

#-- removing large intermediate files --#
rm -f ampFrags_KDE_dif.pkl
rm -f ampFrags_KDE_dif_DBL.pkl
rm -f ampFrags_KDE_dif_DBL_inc.pkl


Writing /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/SIPSimRun_SIPSim-pipeline.sh

In [17]:
!chmod 755 $bashFileTmp

In [ ]:
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file SIPSim_pipeline.log -j 6 --stop-on-error

In [ ]:
%pushmsg "SIPSim pipeline complete: $buildDir"

Summary of simulated data


In [ ]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_SIPSim-summary.sh'
bashFileTmp

In [ ]:
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 

echo "# Plotting taxon abundances"

# plotting 'raw' taxon abundances
Rscript {R_dir}OTU_taxonAbund.R \
    OTU_abs{abs}.txt \
    -r {topTaxaToPlot} \
    -o OTU_abs{abs}

# plotting 'sequenced' taxon abundances
Rscript {R_dir}OTU_taxonAbund.R \
    OTU_abs{abs}_PCR_sub.txt \
    -r {topTaxaToPlot} \
    -o OTU_abs{abs}_PCR_sub

In [ ]:
!chmod 755 $bashFileTmp

In [ ]:
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file SIPSim_summary.log -j 20

HR-SIP


In [ ]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_HRSIP.sh'
bashFileTmp

In [ ]:
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 

# phyloseq
## making phyloseq object from OTU table
Rscript {R_dir}phyloseq_make.R \
    OTU_abs{abs}_PCR_sub_w.txt \
    -s OTU_abs{abs}_PCR_sub_meta.txt \
    > OTU_abs{abs}_PCR_sub.physeq

## filtering phyloseq object to just 'heavy' fractions
Rscript {R_dir}phyloseq_edit.R \
    OTU_abs{abs}_PCR_sub.physeq \
    --BD_min {heavy_BD_min} \
    --BD_max {heavy_BD_max} \
    > OTU_abs{abs}_PCR_sub_filt.physeq

## making ordination
Rscript {R_dir}phyloseq_ordination.R \
    OTU_abs{abs}_PCR_sub_filt.physeq \
    OTU_abs{abs}_PCR_sub_filt_bray-NMDS.pdf

# DESeq2
Rscript {R_dir}phyloseq_DESeq2.R \
    --log2 {log2} \
    --hypo greater \
    --cont 1,3,5 \
    --treat 2,4,6 \
    OTU_abs{abs}_PCR_sub_filt.physeq \
    > OTU_abs{abs}_PCR_sub_filt_DESeq2

In [ ]:
!chmod 755 $bashFileTmp

In [ ]:
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file HR-SIP.log -j 20

In [ ]:
%pushmsg "HR-SIP complete: $buildDir"

MW-HR-SIP


In [ ]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_MWHRSIP.sh'
bashFileTmp

In [ ]:
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 

## HR SIP pipeline
Rscript {R_dir}phyloseq_DESeq2.R \
    --log2 {log2} \
    --hypo greater \
    --cont 1,3,5 \
    --treat 2,4,6 \
    --occur_all 0.0,0.05,0.1,0.15,0.2,0.25,0.3,0.35,0.4,0.45,0.5 \
    -w 1.70-1.73,1.72-1.75,1.74-1.77 \
    --all OTU_abs1e9_PCR_sub_MW-all.txt \
    OTU_abs{abs}_PCR_sub.physeq \
    > OTU_abs{abs}_PCR_sub_filt_MW_DESeq2

In [ ]:
!chmod 755 $bashFileTmp

In [ ]:
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file MW-HR-SIP.log -j 20

In [ ]:
%pushmsg "MW-HR-SIP complete: $buildDir"

q-SIP


In [ ]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_qSIP.sh'
bashFileTmp

In [ ]:
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 
# OPENBLAS threads 
export OMP_NUM_THREADS=1

# qSIP
SIPSim qSIP \
    OTU_abs{abs}.txt \
    OTU_abs{abs}_PCR_sub.txt \
    > OTU_abs{abs}_PCR_sub_qSIP.txt
        

# qSIP: atom excess
SIPSim qSIP_atom_excess \
    --np {np} \
    OTU_abs{abs}_PCR_sub_qSIP.txt \
    {exp_design} \
    > OTU_abs{abs}_PCR_sub_qSIP_atom.txt

In [ ]:
!chmod 755 $bashFileTmp

In [ ]:
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file qSIP.log -j 6

In [ ]:
%pushmsg "q-SIP complete: $buildDir"

delta-BD


In [ ]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_dBD.sh'
bashFileTmp

In [ ]:
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim 
# OPENBLAS threads 
export OMP_NUM_THREADS=1

#deltaBD 
SIPSim deltaBD \
    OTU_abs{abs}_PCR_sub.txt \
    {exp_design} \
    > OTU_abs{abs}_PCR_sub_dBD.txt

In [ ]:
!chmod 755 $bashFileTmp

In [ ]:
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file deltaBD.log -j 20

In [ ]:
%pushmsg "deltaBD complete: $buildDir"

Making confusion matrices


In [ ]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_cMtx.sh'
bashFileTmp

In [ ]:
%%writefile $bashFileTmp
#!/bin/bash
# offset job start to prevent conda activate errors
sleep $[ ( $RANDOM % 10 )  + 1 ]s
source activate SIPSim

# HR-SIP
Rscript {R_dir}DESeq2_confuseMtx.R \
    --libs 2,4,6 \
    --padj {padj} \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub_filt_DESeq2

# HR-SIP multiple 'heavy' BD windows
Rscript {R_dir}DESeq2_confuseMtx.R \
    --libs 2,4,6 \
    --padj {padj} \
    -o DESeq2_multi-cMtx \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub_filt_MW_DESeq2
    
# qSIP    
Rscript {R_dir}qSIP_confuseMtx.R \
    --libs 2,4,6 \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub_qSIP_atom.txt

# heavy-SIP    
Rscript {R_dir}heavy_confuseMtx.R \
    --treat 2,4,6 \
    --con 1,3,5 \
    --method 1 \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub.txt

In [ ]:
!chmod 755 $bashFileTmp

In [ ]:
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file cMtx.log -j 20

Aggregating confusion matrices


In [ ]:
def agg_cMtx(prefix):
    # all data
    x = prefix + '-cMtx_data.txt'
    !nestagg delim \
       -d $buildDir \
       -k shared_perc,perm_perc,rep \
       -o $x \
       --tab \
       $x

    # overall
    x = prefix + '-cMtx_overall.txt'
    !nestagg delim \
        -d $buildDir \
        -k shared_perc,perm_perc,rep \
        -o $x \
        --tab \
        $x

    # by class
    x = prefix + '-cMtx_byClass.txt'
    !nestagg delim \
        -d $buildDir \
        -k shared_perc,perm_perc,rep \
        -o $x \
        --tab \
        $x
        
agg_cMtx('DESeq2')
agg_cMtx('DESeq2_multi')
agg_cMtx('qSIP') 
agg_cMtx('heavy')

In [ ]:
%pushmsg "microBetaDiv complete!"

Calculating pre-fractionation comm beta-div indices


In [60]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_betaDiv.sh'
bashFileTmp


Out[60]:
'/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/SIPSimRun_betaDiv.sh'

In [61]:
%%writefile $bashFileTmp
#!/bin/bash
source activate SIPSim

# beta diversity
Rscript {R_dir}comm_beta_div.R \
    comm.txt \
    > comm_betaDiv.txt


Overwriting /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/SIPSimRun_betaDiv.sh

In [62]:
!chmod 755 $bashFileTmp

In [63]:
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

nestrun --template-file $2 -d $3 --log-file comm_betaDiv.log -j 10


2017-08-20 20:09:43,185 * INFO * Template: ./SIPSimRun_betaDiv.sh
2017-08-20 20:09:43,190 * INFO * [71028] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/1
2017-08-20 20:09:43,195 * INFO * [71031] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/2
2017-08-20 20:09:43,202 * INFO * [71039] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/3
2017-08-20 20:09:43,208 * INFO * [71046] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/4
2017-08-20 20:09:43,214 * INFO * [71057] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/5
2017-08-20 20:09:43,220 * INFO * [71065] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/6
2017-08-20 20:09:43,225 * INFO * [71073] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/7
2017-08-20 20:09:43,229 * INFO * [71079] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/8
2017-08-20 20:09:43,236 * INFO * [71085] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/9
2017-08-20 20:09:43,242 * INFO * [71095] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/10
2017-08-20 20:09:49,666 * INFO * [71031] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/2 Finished with 0
2017-08-20 20:09:49,673 * INFO * [71406] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/1
2017-08-20 20:09:49,920 * INFO * [71095] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/10 Finished with 0
2017-08-20 20:09:49,926 * INFO * [71416] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/2
2017-08-20 20:09:49,942 * INFO * [71073] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/7 Finished with 0
2017-08-20 20:09:49,952 * INFO * [71426] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/3
2017-08-20 20:09:49,969 * INFO * [71079] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/8 Finished with 0
2017-08-20 20:09:49,980 * INFO * [71436] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/4
2017-08-20 20:09:49,998 * INFO * [71057] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/5 Finished with 0
2017-08-20 20:09:50,006 * INFO * [71448] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/5
2017-08-20 20:09:50,006 * INFO * [71065] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/6 Finished with 0
2017-08-20 20:09:50,013 * INFO * [71451] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/6
2017-08-20 20:09:50,027 * INFO * [71028] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/1 Finished with 0
2017-08-20 20:09:50,036 * INFO * [71466] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/7
2017-08-20 20:09:50,078 * INFO * [71085] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/9 Finished with 0
2017-08-20 20:09:50,088 * INFO * [71476] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/8
2017-08-20 20:09:50,219 * INFO * [71039] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/3 Finished with 0
2017-08-20 20:09:50,229 * INFO * [71486] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/9
2017-08-20 20:09:50,501 * INFO * [71046] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/0/4 Finished with 0
2017-08-20 20:09:50,506 * INFO * [71497] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/10
2017-08-20 20:09:55,619 * INFO * [71406] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/1 Finished with 0
2017-08-20 20:09:55,628 * INFO * [71796] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/1
2017-08-20 20:09:56,018 * INFO * [71448] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/5 Finished with 0
2017-08-20 20:09:56,035 * INFO * [71806] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/2
2017-08-20 20:09:56,333 * INFO * [71436] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/4 Finished with 0
2017-08-20 20:09:56,341 * INFO * [71819] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/3
2017-08-20 20:09:56,343 * INFO * [71451] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/6 Finished with 0
2017-08-20 20:09:56,348 * INFO * [71821] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/4
2017-08-20 20:09:56,398 * INFO * [71426] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/3 Finished with 0
2017-08-20 20:09:56,403 * INFO * [71837] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/5
2017-08-20 20:09:56,426 * INFO * [71466] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/7 Finished with 0
2017-08-20 20:09:56,434 * INFO * [71847] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/6
2017-08-20 20:09:56,444 * INFO * [71416] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/2 Finished with 0
2017-08-20 20:09:56,453 * INFO * [71859] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/7
2017-08-20 20:09:56,453 * INFO * [71476] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/8 Finished with 0
2017-08-20 20:09:56,461 * INFO * [71864] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/8
2017-08-20 20:09:56,590 * INFO * [71497] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/10 Finished with 0
2017-08-20 20:09:56,598 * INFO * [71887] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/9
2017-08-20 20:09:56,988 * INFO * [71486] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/5/9 Finished with 0
2017-08-20 20:09:56,995 * INFO * [71900] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/10
2017-08-20 20:10:02,182 * INFO * [71796] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/1 Finished with 0
2017-08-20 20:10:02,203 * INFO * [72187] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/1
2017-08-20 20:10:02,337 * INFO * [71819] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/3 Finished with 0
2017-08-20 20:10:02,350 * INFO * [72197] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/2
2017-08-20 20:10:02,402 * INFO * [71806] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/2 Finished with 0
2017-08-20 20:10:02,412 * INFO * [72207] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/3
2017-08-20 20:10:02,481 * INFO * [71821] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/4 Finished with 0
2017-08-20 20:10:02,493 * INFO * [72217] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/4
2017-08-20 20:10:02,585 * INFO * [71887] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/9 Finished with 0
2017-08-20 20:10:02,594 * INFO * [72227] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/5
2017-08-20 20:10:02,753 * INFO * [71847] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/6 Finished with 0
2017-08-20 20:10:02,763 * INFO * [72237] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/6
2017-08-20 20:10:02,940 * INFO * [71864] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/8 Finished with 0
2017-08-20 20:10:02,946 * INFO * [72248] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/7
2017-08-20 20:10:03,051 * INFO * [71859] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/7 Finished with 0
2017-08-20 20:10:03,060 * INFO * [72258] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/8
2017-08-20 20:10:03,438 * INFO * [71837] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/5 Finished with 0
2017-08-20 20:10:03,443 * INFO * [72296] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/9
2017-08-20 20:10:03,788 * INFO * [71900] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/10/10 Finished with 0
2017-08-20 20:10:03,801 * INFO * [72337] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/10
2017-08-20 20:10:08,402 * INFO * [72187] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/1 Finished with 0
2017-08-20 20:10:08,413 * INFO * [72580] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/1
2017-08-20 20:10:08,873 * INFO * [72227] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/5 Finished with 0
2017-08-20 20:10:08,881 * INFO * [72590] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/2
2017-08-20 20:10:08,967 * INFO * [72237] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/6 Finished with 0
2017-08-20 20:10:08,978 * INFO * [72600] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/3
2017-08-20 20:10:09,023 * INFO * [72217] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/4 Finished with 0
2017-08-20 20:10:09,031 * INFO * [72611] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/4
2017-08-20 20:10:09,039 * INFO * [72207] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/3 Finished with 0
2017-08-20 20:10:09,045 * INFO * [72620] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/5
2017-08-20 20:10:09,108 * INFO * [72248] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/7 Finished with 0
2017-08-20 20:10:09,117 * INFO * [72631] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/6
2017-08-20 20:10:09,204 * INFO * [72197] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/2 Finished with 0
2017-08-20 20:10:09,211 * INFO * [72641] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/7
2017-08-20 20:10:09,353 * INFO * [72296] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/9 Finished with 0
2017-08-20 20:10:09,361 * INFO * [72653] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/8
2017-08-20 20:10:09,534 * INFO * [72258] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/8 Finished with 0
2017-08-20 20:10:09,542 * INFO * [72671] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/9
2017-08-20 20:10:09,853 * INFO * [72337] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/15/10 Finished with 0
2017-08-20 20:10:09,857 * INFO * [72690] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/10
2017-08-20 20:10:14,666 * INFO * [72580] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/1 Finished with 0
2017-08-20 20:10:14,677 * INFO * [72979] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/1
2017-08-20 20:10:14,937 * INFO * [72590] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/2 Finished with 0
2017-08-20 20:10:14,944 * INFO * [72989] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/2
2017-08-20 20:10:14,977 * INFO * [72620] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/5 Finished with 0
2017-08-20 20:10:14,984 * INFO * [72999] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/3
2017-08-20 20:10:15,007 * INFO * [72600] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/3 Finished with 0
2017-08-20 20:10:15,020 * INFO * [73009] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/4
2017-08-20 20:10:15,224 * INFO * [72611] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/4 Finished with 0
2017-08-20 20:10:15,234 * INFO * [73019] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/5
2017-08-20 20:10:15,378 * INFO * [72653] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/8 Finished with 0
2017-08-20 20:10:15,383 * INFO * [73030] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/6
2017-08-20 20:10:15,504 * INFO * [72631] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/6 Finished with 0
2017-08-20 20:10:15,511 * INFO * [73040] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/7
2017-08-20 20:10:15,581 * INFO * [72641] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/7 Finished with 0
2017-08-20 20:10:15,589 * INFO * [73052] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/8
2017-08-20 20:10:15,708 * INFO * [72671] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/9 Finished with 0
2017-08-20 20:10:15,717 * INFO * [73073] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/9
2017-08-20 20:10:15,968 * INFO * [72690] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/80/20/10 Finished with 0
2017-08-20 20:10:15,977 * INFO * [73098] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/10
2017-08-20 20:10:20,896 * INFO * [72999] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/3 Finished with 0
2017-08-20 20:10:20,900 * INFO * [73369] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/1
2017-08-20 20:10:21,154 * INFO * [72979] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/1 Finished with 0
2017-08-20 20:10:21,162 * INFO * [73379] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/2
2017-08-20 20:10:21,249 * INFO * [73030] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/6 Finished with 0
2017-08-20 20:10:21,257 * INFO * [73389] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/3
2017-08-20 20:10:21,363 * INFO * [72989] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/2 Finished with 0
2017-08-20 20:10:21,368 * INFO * [73401] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/4
2017-08-20 20:10:21,371 * INFO * [73040] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/7 Finished with 0
2017-08-20 20:10:21,376 * INFO * [73409] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/5
2017-08-20 20:10:21,388 * INFO * [73009] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/4 Finished with 0
2017-08-20 20:10:21,396 * INFO * [73419] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/6
2017-08-20 20:10:21,420 * INFO * [73019] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/5 Finished with 0
2017-08-20 20:10:21,428 * INFO * [73429] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/5/7
2017-08-20 20:10:21,874 * INFO * [73052] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/85/0/8 Finished with 0
2017-08-20 20:10:21,881 * INFO * [73451] Started ./SIPSimRun_betaDiv.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDi
limit_output extension: Maximum message size of 20000 exceeded with 79016 characters

--End of simulation--


Results


In [64]:
F = os.path.join(buildDir, '*-cMtx_byClass.txt')
files = glob.glob(F)
files


Out[64]:
['/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/DESeq2-cMtx_byClass.txt',
 '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/DESeq2_multi-cMtx_byClass.txt',
 '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/qSIP-cMtx_byClass.txt',
 '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/microBetaDiv/heavy-cMtx_byClass.txt']

In [65]:
# checking for errors
!find $buildDir -name "*log" | wc -l
!find $buildDir -name "*log" | xargs grep -i error


2250

In [ ]: