Goal

Accuracy as a function of isotope incorporation & sampling depth

acc ~ depth + incorp

Variable parameters:

  • atom % isotope incorporation
    • 0, 15, 25, 50, 75, 100
  • sampling depth
    • 1e2, 1e3, 1e4, 1e5
  • n-reps (stocastic: taxon abundances & which incorporate)
    • 10

Setting paths


In [8]:
# paths
import os

workDir = '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/'
buildDir = os.path.join(workDir, 'atomIncorp_sampDepth')
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 [9]:
import glob
import itertools
import nestly

In [10]:
%load_ext pushmsg


The pushmsg extension is already loaded. To reload it, use:
  %reload_ext pushmsg

In [11]:
if not os.path.isdir(buildDir):
    os.makedirs(buildDir)
%cd $buildDir


/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth

BD min/max


In [12]:
## 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 [13]:
# 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 [14]:
# building tree structure
nest = nestly.Nest()

# varying params: TEST
#nest.add('percIncorp', [0, 100])
#nest.add('subsample_size', [100, 10000])
#nest.add('rep', [1])

# varying params
nest.add('percIncorp', [0, 15, 25, 50, 75, 100])
nest.add('subsample_size', [100, 1000, 10000, 100000])
nest.add('rep', range(1,11))


## set params
nest.add('percTaxa', [10], create_dir=False)
nest.add('abs', ['1e9'], create_dir=False)
#nest.add('abs', ['1e7'], create_dir=False)   # TESTING
nest.add('np', [4], create_dir=False)
nest.add('Monte_rep', [100000], create_dir=False)
nest.add('subsample_dist', ['uniform'], 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/atomIncorp_sampDepth/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 \
    --config incorp.config \
    {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/atomIncorp_sampDepth/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


2017-07-30 15:16:48,135 * INFO * Template: ./SIPSimRun_expDesign.sh
2017-07-30 15:16:48,140 * INFO * [44847] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/1
2017-07-30 15:16:48,145 * INFO * [44850] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/2
2017-07-30 15:16:48,149 * INFO * [44858] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/3
2017-07-30 15:16:48,156 * INFO * [44866] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/4
2017-07-30 15:16:48,160 * INFO * [44874] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/5
2017-07-30 15:16:48,167 * INFO * [44885] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/6
2017-07-30 15:16:48,171 * INFO * [44890] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/7
2017-07-30 15:16:48,177 * INFO * [44900] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/8
2017-07-30 15:16:48,184 * INFO * [44908] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/9
2017-07-30 15:16:48,189 * INFO * [44916] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/10
2017-07-30 15:16:48,195 * INFO * [44924] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/1
2017-07-30 15:16:48,201 * INFO * [44931] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/2
2017-07-30 15:16:48,207 * INFO * [44940] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/3
2017-07-30 15:16:48,214 * INFO * [44946] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/4
2017-07-30 15:16:48,221 * INFO * [44958] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/5
2017-07-30 15:16:48,226 * INFO * [44964] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/6
2017-07-30 15:16:48,234 * INFO * [44972] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/7
2017-07-30 15:16:48,241 * INFO * [44980] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/8
2017-07-30 15:16:48,246 * INFO * [44986] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/9
2017-07-30 15:16:48,254 * INFO * [44994] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/10
2017-07-30 15:17:01,916 * INFO * [44916] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/10 Finished with 0
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2017-07-30 15:17:01,954 * INFO * [44964] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/6 Finished with 0
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2017-07-30 15:17:01,998 * INFO * [44866] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/4 Finished with 0
2017-07-30 15:17:02,021 * INFO * [45647] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/3
2017-07-30 15:17:02,021 * INFO * [44890] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/7 Finished with 0
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2017-07-30 15:17:02,026 * INFO * [44900] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/8 Finished with 0
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2017-07-30 15:17:02,032 * INFO * [44885] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/6 Finished with 0
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2017-07-30 15:17:02,044 * INFO * [44931] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/2 Finished with 0
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2017-07-30 15:17:02,066 * INFO * [44858] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/3 Finished with 0
2017-07-30 15:17:02,073 * INFO * [45687] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/8
2017-07-30 15:17:02,074 * INFO * [44994] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/10 Finished with 0
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2017-07-30 15:17:02,087 * INFO * [44850] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/2 Finished with 0
2017-07-30 15:17:02,093 * INFO * [45698] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/10
2017-07-30 15:17:02,095 * INFO * [44924] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/1 Finished with 0
2017-07-30 15:17:02,102 * INFO * [45710] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/1
2017-07-30 15:17:02,137 * INFO * [44940] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/3 Finished with 0
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2017-07-30 15:17:02,176 * INFO * [44908] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/9 Finished with 0
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2017-07-30 15:17:02,183 * INFO * [44980] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/8 Finished with 0
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2017-07-30 15:17:02,189 * INFO * [44946] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/4 Finished with 0
2017-07-30 15:17:02,198 * INFO * [45738] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/5
2017-07-30 15:17:02,198 * INFO * [44847] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/1 Finished with 0
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2017-07-30 15:17:02,203 * INFO * [44958] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/5 Finished with 0
2017-07-30 15:17:02,208 * INFO * [45755] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/7
2017-07-30 15:17:02,212 * INFO * [44972] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/7 Finished with 0
2017-07-30 15:17:02,219 * INFO * [45767] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/8
2017-07-30 15:17:02,220 * INFO * [44874] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/5 Finished with 0
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2017-07-30 15:17:02,243 * INFO * [44986] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/9 Finished with 0
2017-07-30 15:17:02,251 * INFO * [45783] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/10
2017-07-30 15:17:12,319 * INFO * [45639] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/2 Finished with 0
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2017-07-30 15:17:12,396 * INFO * [45671] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/6 Finished with 0
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2017-07-30 15:17:12,428 * INFO * [45628] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/1 Finished with 0
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2017-07-30 15:17:12,465 * INFO * [45755] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/7 Finished with 0
2017-07-30 15:17:12,472 * INFO * [46441] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/4
2017-07-30 15:17:12,472 * INFO * [45660] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/5 Finished with 0
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2017-07-30 15:17:12,478 * INFO * [45698] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/10 Finished with 0
2017-07-30 15:17:12,491 * INFO * [46453] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/6
2017-07-30 15:17:12,491 * INFO * [45677] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/7 Finished with 0
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2017-07-30 15:17:12,498 * INFO * [45687] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/8 Finished with 0
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2017-07-30 15:17:12,505 * INFO * [45650] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/4 Finished with 0
2017-07-30 15:17:12,510 * INFO * [46477] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/9
2017-07-30 15:17:12,510 * INFO * [45719] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/2 Finished with 0
2017-07-30 15:17:12,516 * INFO * [46484] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/10
2017-07-30 15:17:12,516 * INFO * [45691] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/9 Finished with 0
2017-07-30 15:17:12,522 * INFO * [46494] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/1
2017-07-30 15:17:12,523 * INFO * [45647] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/3 Finished with 0
2017-07-30 15:17:12,531 * INFO * [46504] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/2
2017-07-30 15:17:12,537 * INFO * [45738] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/5 Finished with 0
2017-07-30 15:17:12,543 * INFO * [46513] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/3
2017-07-30 15:17:12,574 * INFO * [45774] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/9 Finished with 0
2017-07-30 15:17:12,581 * INFO * [46521] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/4
2017-07-30 15:17:12,582 * INFO * [45710] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/1 Finished with 0
2017-07-30 15:17:12,587 * INFO * [46524] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/5
2017-07-30 15:17:12,629 * INFO * [45767] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/8 Finished with 0
2017-07-30 15:17:12,636 * INFO * [46537] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/6
2017-07-30 15:17:12,640 * INFO * [45783] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/10 Finished with 0
2017-07-30 15:17:12,650 * INFO * [46545] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/7
2017-07-30 15:17:12,650 * INFO * [45727] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/3 Finished with 0
2017-07-30 15:17:12,659 * INFO * [46552] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/8
2017-07-30 15:17:12,659 * INFO * [45730] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/4 Finished with 0
2017-07-30 15:17:12,664 * INFO * [46558] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/9
2017-07-30 15:17:12,664 * INFO * [45746] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/6 Finished with 0
2017-07-30 15:17:12,674 * INFO * [46569] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/10
2017-07-30 15:17:22,543 * INFO * [46433] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/3 Finished with 0
2017-07-30 15:17:22,549 * INFO * [47198] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/1
2017-07-30 15:17:22,709 * INFO * [46462] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/7 Finished with 0
2017-07-30 15:17:22,714 * INFO * [47206] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/2
2017-07-30 15:17:22,714 * INFO * [46444] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/5 Finished with 0
2017-07-30 15:17:22,722 * INFO * [47211] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/3
2017-07-30 15:17:22,723 * INFO * [46484] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/10 Finished with 0
2017-07-30 15:17:22,729 * INFO * [47219] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/4
2017-07-30 15:17:22,746 * INFO * [46468] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/8 Finished with 0
2017-07-30 15:17:22,764 * INFO * [47230] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/5
2017-07-30 15:17:22,765 * INFO * [46494] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/1 Finished with 0
2017-07-30 15:17:22,769 * INFO * [47233] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/6
2017-07-30 15:17:22,777 * INFO * [46417] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/1 Finished with 0
2017-07-30 15:17:22,782 * INFO * [47246] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/7
2017-07-30 15:17:22,796 * INFO * [46477] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/9 Finished with 0
2017-07-30 15:17:22,809 * INFO * [47254] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/8
2017-07-30 15:17:22,809 * INFO * [46441] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/4 Finished with 0
2017-07-
limit_output extension: Maximum message size of 20000 exceeded with 67908 characters

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

SIPSim pipeline


In [14]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_SIPSim-pipeline.sh'
bashFileTmp


Out[14]:
'/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/SIPSimRun_SIPSim-pipeline.sh'

In [15]:
%%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 low:{subsample_size},high:{subsample_size} \
    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/atomIncorp_sampDepth/SIPSimRun_SIPSim-pipeline.sh

In [16]:
!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 [60]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_MWHRSIP.sh'
bashFileTmp


Out[60]:
'/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/SIPSimRun_MWHRSIP.sh'

In [61]:
%%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


Overwriting /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/SIPSimRun_MWHRSIP.sh

In [62]:
!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 [15]:
bashFileTmp = os.path.splitext(bashFile)[0] + '_cMtx.sh'
bashFileTmp


Out[15]:
'/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/SIPSimRun_cMtx.sh'

In [16]:
%%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


Overwriting /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/SIPSimRun_cMtx.sh

In [17]:
!chmod 755 $bashFileTmp

In [18]:
%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

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


2017-08-21 19:58:50,422 * INFO * Template: ./SIPSimRun_cMtx.sh
2017-08-21 19:58:50,427 * INFO * [42752] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/1
2017-08-21 19:58:50,432 * INFO * [42754] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/2
2017-08-21 19:58:50,437 * INFO * [42756] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/3
2017-08-21 19:58:50,443 * INFO * [42758] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/4
2017-08-21 19:58:50,448 * INFO * [42760] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/5
2017-08-21 19:58:50,455 * INFO * [42762] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/6
2017-08-21 19:58:50,461 * INFO * [42764] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/7
2017-08-21 19:58:50,468 * INFO * [42766] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/8
2017-08-21 19:58:50,475 * INFO * [42768] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/9
2017-08-21 19:58:50,481 * INFO * [42770] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/10
2017-08-21 19:58:50,488 * INFO * [42772] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/1
2017-08-21 19:58:50,493 * INFO * [42774] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/2
2017-08-21 19:58:50,497 * INFO * [42776] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/3
2017-08-21 19:58:50,503 * INFO * [42778] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/4
2017-08-21 19:58:50,508 * INFO * [42780] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/5
2017-08-21 19:58:50,516 * INFO * [42782] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/6
2017-08-21 19:58:50,522 * INFO * [42784] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/7
2017-08-21 19:58:50,528 * INFO * [42786] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/8
2017-08-21 19:58:50,536 * INFO * [42788] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/9
2017-08-21 19:58:50,542 * INFO * [42790] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/10
2017-08-21 19:59:14,749 * INFO * [42774] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/2 Finished with 0
2017-08-21 19:59:14,756 * INFO * [43934] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/1
2017-08-21 19:59:15,476 * INFO * [42760] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/5 Finished with 0
2017-08-21 19:59:15,483 * INFO * [43962] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/2
2017-08-21 19:59:16,320 * INFO * [42780] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/5 Finished with 0
2017-08-21 19:59:16,330 * INFO * [43982] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/3
2017-08-21 19:59:17,399 * INFO * [42768] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/9 Finished with 0
2017-08-21 19:59:17,405 * INFO * [44002] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/4
2017-08-21 19:59:18,208 * INFO * [42782] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/6 Finished with 0
2017-08-21 19:59:18,212 * INFO * [44014] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/5
2017-08-21 19:59:18,501 * INFO * [42776] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/3 Finished with 0
2017-08-21 19:59:18,509 * INFO * [44025] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/6
2017-08-21 19:59:18,536 * INFO * [42788] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/9 Finished with 0
2017-08-21 19:59:18,545 * INFO * [44031] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/7
2017-08-21 19:59:18,546 * INFO * [42766] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/8 Finished with 0
2017-08-21 19:59:18,552 * INFO * [44033] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/8
2017-08-21 19:59:19,425 * INFO * [42786] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/8 Finished with 0
2017-08-21 19:59:19,430 * INFO * [44038] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/9
2017-08-21 19:59:19,677 * INFO * [42756] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/3 Finished with 0
2017-08-21 19:59:19,684 * INFO * [44042] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/10
2017-08-21 19:59:19,933 * INFO * [42784] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/7 Finished with 0
2017-08-21 19:59:19,940 * INFO * [44056] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/1
2017-08-21 19:59:22,054 * INFO * [42752] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/1 Finished with 0
2017-08-21 19:59:22,061 * INFO * [44086] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/2
2017-08-21 19:59:22,928 * INFO * [42758] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/4 Finished with 0
2017-08-21 19:59:22,934 * INFO * [44103] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/3
2017-08-21 19:59:23,163 * INFO * [42770] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/10 Finished with 0
2017-08-21 19:59:23,172 * INFO * [44112] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/4
2017-08-21 19:59:23,247 * INFO * [42790] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/10 Finished with 0
2017-08-21 19:59:23,256 * INFO * [44116] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/5
2017-08-21 19:59:23,342 * INFO * [42764] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/7 Finished with 0
2017-08-21 19:59:23,348 * INFO * [44120] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/6
2017-08-21 19:59:23,969 * INFO * [42754] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/2 Finished with 0
2017-08-21 19:59:23,976 * INFO * [44141] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/7
2017-08-21 19:59:24,105 * INFO * [42778] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/4 Finished with 0
2017-08-21 19:59:24,116 * INFO * [44145] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/8
2017-08-21 19:59:24,642 * INFO * [42762] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100/6 Finished with 0
2017-08-21 19:59:24,649 * INFO * [44164] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/9
2017-08-21 19:59:26,075 * INFO * [42772] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/1000/1 Finished with 0
2017-08-21 19:59:26,086 * INFO * [44237] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/10
2017-08-21 19:59:44,003 * INFO * [43962] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/2 Finished with 0
2017-08-21 19:59:44,014 * INFO * [45182] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/1
2017-08-21 19:59:45,252 * INFO * [44025] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/6 Finished with 0
2017-08-21 19:59:45,259 * INFO * [45226] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/2
2017-08-21 19:59:47,877 * INFO * [44038] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/9 Finished with 0
2017-08-21 19:59:47,884 * INFO * [45272] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/3
2017-08-21 19:59:48,530 * INFO * [44056] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/1 Finished with 0
2017-08-21 19:59:48,536 * INFO * [45278] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/4
2017-08-21 19:59:48,993 * INFO * [44141] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/7 Finished with 0
2017-08-21 19:59:49,000 * INFO * [45289] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/5
2017-08-21 19:59:49,026 * INFO * [44031] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/7 Finished with 0
2017-08-21 19:59:49,032 * INFO * [45293] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/6
2017-08-21 19:59:49,299 * INFO * [43982] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/3 Finished with 0
2017-08-21 19:59:49,307 * INFO * [45303] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/7
2017-08-21 19:59:49,455 * INFO * [43934] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/1 Finished with 0
2017-08-21 19:59:49,464 * INFO * [45315] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/8
2017-08-21 19:59:50,568 * INFO * [44002] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/4 Finished with 0
2017-08-21 19:59:50,576 * INFO * [45385] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/9
2017-08-21 19:59:50,891 * INFO * [44116] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/5 Finished with 0
2017-08-21 19:59:50,904 * INFO * [45395] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/10
2017-08-21 19:59:51,273 * INFO * [44014] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/5 Finished with 0
2017-08-21 19:59:51,282 * INFO * [45411] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/1
2017-08-21 19:59:51,517 * INFO * [44120] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/6 Finished with 0
2017-08-21 19:59:51,530 * INFO * [45429] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/2
2017-08-21 19:59:51,760 * INFO * [44042] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/10 Finished with 0
2017-08-21 19:59:51,798 * INFO * [45434] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/3
2017-08-21 19:59:52,341 * INFO * [44033] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/10000/8 Finished with 0
2017-08-21 19:59:52,349 * INFO * [45466] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/4
2017-08-21 19:59:53,160 * INFO * [44103] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/3 Finished with 0
2017-08-21 19:59:53,169 * INFO * [45502] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/5
2017-08-21 19:59:55,492 * INFO * [44164] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/9 Finished with 0
2017-08-21 19:59:55,502 * INFO * [45604] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/6
2017-08-21 19:59:56,569 * INFO * [44112] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/4 Finished with 0
2017-08-21 19:59:56,579 * INFO * [45664] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/7
2017-08-21 19:59:57,152 * INFO * [44086] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/2 Finished with 0
2017-08-21 19:59:57,161 * INFO * [45691] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/8
2017-08-21 19:59:57,646 * INFO * [44145] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/8 Finished with 0
2017-08-21 19:59:57,657 * INFO * [45726] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/9
2017-08-21 19:59:58,602 * INFO * [44237] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/0/100000/10 Finished with 0
2017-08-21 19:59:58,613 * INFO * [45820] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/10
2017-08-21 20:00:09,695 * INFO * [45226] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/2 Finished with 0
2017-08-21 20:00:09,708 * INFO * [46388] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/1
2017-08-21 20:00:13,174 * INFO * [45272] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/3 Finished with 0
2017-08-21 20:00:13,181 * INFO * [46456] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/2
2017-08-21 20:00:14,190 * INFO * [45278] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/4 Finished with 0
2017-08-21 20:00:14,199 * INFO * [46510] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/3
2017-08-21 20:00:14,205 * INFO * [45303] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/7 Finished with 0
2017-08-21 20:00:14,213 * INFO * [46516] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/4
2017-08-21 20:00:15,337 * INFO * [45289] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/5 Finished with 0
2017-08-21 20:00:15,348 * INFO * [46575] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/5
2017-08-21 20:00:17,451 * INFO * [45182] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/1 Finished with 0
2017-08-21 20:00:17,458 * INFO * [46632] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/6
2017-08-21 20:00:17,529 * INFO * [45411] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/1 Finished with 0
2017-08-21 20:00:17,537 * INFO * [46636] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/7
2017-08-21 20:00:17,738 * INFO * [45293] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/6 Finished with 0
2017-08-21 20:00:17,743 * INFO * [46640] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/8
2017-08-21 20:00:17,923 * INFO * [45434] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/1000/3 Finished with 0
2017-08-21 20:00:17,928 * INFO * [46654] Started ./SIPSimRun_cMtx.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/10000/9
2017-08-21 20:00:20,805 * INFO * [45395] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/15/100/10 Finished with 0
2017-08-21 20:00:20
limit_output extension: Maximum message size of 20000 exceeded with 80271 characters

Aggregating confusion matrices


In [19]:
def agg_cMtx(prefix):
    # all data
    x = prefix + '-cMtx_data.txt'
    !nestagg delim \
       -d $buildDir \
       -k percIncorp,subsample_size,rep \
       -o $x \
       --tab \
       $x

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

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

In [20]:
%pushmsg "atomIncorp_sampleDepth complete!"

--End of simulation--


Results


In [21]:
F = os.path.join(buildDir, '*-cMtx_byClass.txt')
files = glob.glob(F)
files


Out[21]:
['/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/DESeq2-cMtx_byClass.txt',
 '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/DESeq2_multi-cMtx_byClass.txt',
 '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/qSIP-cMtx_byClass.txt',
 '/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_sampDepth/heavy-cMtx_byClass.txt']

In [22]:
# checking for errors
!find $buildDir -name "*log" | wc -l
!find $buildDir -name "*log" | xargs grep -i error


1921

In [ ]: