notebook.community

Edit and run

Goal

Accuracy as a function of isotope incorporation & sampling depth

acc ~ n_incorp + perc_incorp

Variable parameters:

  • atom % isotope incorporation
    • 0, 15, 25, 50, 75, 100
  • % taxa as incorporators
    • 1, 5, 10, 25, 50
  • 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, 'atomIncorp_taxaIncorp')
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/atomIncorp_taxaIncorp

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 [6]:



    


# 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 [7]:



    


# building tree structure
nest = nestly.Nest()

# varying params: test
#nest.add('percIncorp', [50])
#nest.add('percTaxa', [10])
#nest.add('rep', [1])

# varying params
nest.add('percIncorp', [0, 15, 25, 50, 75, 100])
nest.add('percTaxa', [1, 5, 10, 25, 50])
nest.add('rep', range(1,11))

## set params
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 [8]:



    


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



    


















    
Out[8]:








'/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/SIPSimRun_expDesign.sh'

















In [9]:



    


%%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_taxaIncorp/SIPSimRun_expDesign.sh

















In [10]:



    


!chmod 755 $bashFileTmp



    











In [11]:



    


%%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



    


















    






2017-08-14 19:58:18,435 * INFO * Template: ./SIPSimRun_expDesign.sh
2017-08-14 19:58:18,440 * INFO * [46537] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/1
2017-08-14 19:58:18,445 * INFO * [46540] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/2
2017-08-14 19:58:18,449 * INFO * [46547] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/3
2017-08-14 19:58:18,454 * INFO * [46556] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/4
2017-08-14 19:58:18,461 * INFO * [46566] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/5
2017-08-14 19:58:18,467 * INFO * [46572] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/6
2017-08-14 19:58:18,472 * INFO * [46583] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/7
2017-08-14 19:58:18,478 * INFO * [46588] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/8
2017-08-14 19:58:18,483 * INFO * [46598] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/9
2017-08-14 19:58:18,489 * INFO * [46604] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/10
2017-08-14 19:58:18,493 * INFO * [46612] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/1
2017-08-14 19:58:18,498 * INFO * [46620] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/2
2017-08-14 19:58:18,502 * INFO * [46628] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/3
2017-08-14 19:58:18,507 * INFO * [46637] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/4
2017-08-14 19:58:18,513 * INFO * [46644] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/5
2017-08-14 19:58:18,520 * INFO * [46654] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/6
2017-08-14 19:58:18,525 * INFO * [46660] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/7
2017-08-14 19:58:18,532 * INFO * [46671] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/8
2017-08-14 19:58:18,547 * INFO * [46679] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/9
2017-08-14 19:58:18,554 * INFO * [46686] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/10
2017-08-14 19:58:31,981 * INFO * [46588] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/8 Finished with 0
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2017-08-14 19:58:32,001 * INFO * [46671] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/8 Finished with 0
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2017-08-14 19:58:32,103 * INFO * [46654] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/6 Finished with 0
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2017-08-14 19:58:32,109 * INFO * [46686] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/10 Finished with 0
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2017-08-14 19:58:32,124 * INFO * [46660] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/7 Finished with 0
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2017-08-14 19:58:32,167 * INFO * [46679] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/9 Finished with 0
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2017-08-14 19:58:32,188 * INFO * [46598] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/9 Finished with 0
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2017-08-14 19:58:32,202 * INFO * [46556] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/4 Finished with 0
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2017-08-14 19:58:32,209 * INFO * [46604] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/10 Finished with 0
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2017-08-14 19:58:32,219 * INFO * [46612] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/1 Finished with 0
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2017-08-14 19:58:32,235 * INFO * [46572] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/6 Finished with 0
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2017-08-14 19:58:32,252 * INFO * [46537] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/1 Finished with 0
2017-08-14 19:58:32,258 * INFO * [47405] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/2
2017-08-14 19:58:32,302 * INFO * [46637] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/4 Finished with 0
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2017-08-14 19:58:32,311 * INFO * [46547] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/3 Finished with 0
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2017-08-14 19:58:32,320 * INFO * [46540] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/2 Finished with 0
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2017-08-14 19:58:32,327 * INFO * [46566] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/5 Finished with 0
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2017-08-14 19:58:32,335 * INFO * [46628] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/3 Finished with 0
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2017-08-14 19:58:32,347 * INFO * [46620] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/2 Finished with 0
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2017-08-14 19:58:32,363 * INFO * [46583] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/1/7 Finished with 0
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2017-08-14 19:58:32,371 * INFO * [46644] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/5/5 Finished with 0
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2017-08-14 19:58:42,265 * INFO * [47317] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/1 Finished with 0
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2017-08-14 19:58:42,289 * INFO * [47333] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/3 Finished with 0
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2017-08-14 19:58:42,344 * INFO * [47325] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/2 Finished with 0
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2017-08-14 19:58:42,446 * INFO * [47344] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/5 Finished with 0
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2017-08-14 19:58:42,489 * INFO * [47365] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/7 Finished with 0
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2017-08-14 19:58:42,526 * INFO * [47376] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/9 Finished with 0
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2017-08-14 19:58:42,532 * INFO * [47336] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/4 Finished with 0
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2017-08-14 19:58:42,551 * INFO * [47426] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/5 Finished with 0
2017-08-14 19:58:42,556 * INFO * [48149] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/8
2017-08-14 19:58:42,562 * INFO * [47387] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/10 Finished with 0
2017-08-14 19:58:42,567 * INFO * [48161] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/9
2017-08-14 19:58:42,598 * INFO * [47357] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/6 Finished with 0
2017-08-14 19:58:42,606 * INFO * [48169] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/10
2017-08-14 19:58:42,612 * INFO * [47413] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/3 Finished with 0
2017-08-14 19:58:42,618 * INFO * [48177] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/1
2017-08-14 19:58:42,619 * INFO * [47397] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/1 Finished with 0
2017-08-14 19:58:42,626 * INFO * [48182] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/2
2017-08-14 19:58:42,628 * INFO * [47434] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/6 Finished with 0
2017-08-14 19:58:42,643 * INFO * [48193] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/3
2017-08-14 19:58:42,643 * INFO * [47453] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/8 Finished with 0
2017-08-14 19:58:42,649 * INFO * [48196] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/4
2017-08-14 19:58:42,654 * INFO * [47441] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/7 Finished with 0
2017-08-14 19:58:42,661 * INFO * [48209] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/5
2017-08-14 19:58:42,713 * INFO * [47405] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/2 Finished with 0
2017-08-14 19:58:42,719 * INFO * [48217] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/6
2017-08-14 19:58:42,719 * INFO * [47461] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/9 Finished with 0
2017-08-14 19:58:42,725 * INFO * [48220] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/7
2017-08-14 19:58:42,727 * INFO * [47420] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/4 Finished with 0
2017-08-14 19:58:42,733 * INFO * [48232] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/8
2017-08-14 19:58:42,743 * INFO * [47373] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/10/8 Finished with 0
2017-08-14 19:58:42,748 * INFO * [48241] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/9
2017-08-14 19:58:42,805 * INFO * [47465] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/25/10 Finished with 0
2017-08-14 19:58:42,811 * INFO * [48249] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/10
2017-08-14 19:58:52,495 * INFO * [48097] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/1 Finished with 0
2017-08-14 19:58:52,511 * INFO * [48878] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/5/1
2017-08-14 19:58:52,621 * INFO * [48121] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/4 Finished with 0
2017-08-14 19:58:52,626 * INFO * [48887] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/5/2
2017-08-14 19:58:52,712 * INFO * [48113] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/3 Finished with 0
2017-08-14 19:58:52,717 * INFO * [48895] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/5/3
2017-08-14 19:58:52,750 * INFO * [48169] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/10 Finished with 0
2017-08-14 19:58:52,764 * INFO * [48903] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/5/4
2017-08-14 19:58:52,786 * INFO * [48105] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/2 Finished with 0
2017-08-14 19:58:52,793 * INFO * [48911] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/5/5
2017-08-14 19:58:52,824 * INFO * [48149] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/8 Finished with 0
2017-08-14 19:58:52,829 * INFO * [48919] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/5/6
2017-08-14 19:58:52,831 * INFO * [48137] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/6 Finished with 0
2017-08-14 19:58:52,837 * INFO * [48922] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/5/7
2017-08-14 19:58:52,856 * INFO * [48177] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/1/1 Finished with 0
2017-08-14 19:58:52,866 * INFO * [48935] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/5/8
2017-08-14 19:58:52,870 * INFO * [48129] /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/0/50/5 Finished with 0
2017-08-14 19:58:52,874 * INFO * [48940] Started ./SIPSimRun_expDesign.sh in /ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/15/5/9
2017-08-14 19:58:52,882 * INFO * [48142] /ebio/abt3_pro









    






limit_output extension: Maximum message size of 20000 exceeded with 100688 characters
















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%pushmsg "exp_design complete: $buildDir"

SIPSim pipeline





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



    


















    
Out[13]:








'/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/SIPSimRun_SIPSim-pipeline.sh'

















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%%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/atomIncorp_taxaIncorp/SIPSimRun_SIPSim-pipeline.sh

















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!chmod 755 $bashFileTmp



    











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%%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



    











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%pushmsg "SIPSim pipeline complete: $buildDir"

Summary of simulated data





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



    











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%%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



    











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!chmod 755 $bashFileTmp



    











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%%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





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



    











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%%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



    











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!chmod 755 $bashFileTmp



    











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%%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



    











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%pushmsg "HR-SIP complete: $buildDir"

MW-HR-SIP





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



    











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%%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



    











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!chmod 755 $bashFileTmp



    











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%%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



    











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%pushmsg "MW-HR-SIP complete: $buildDir"

q-SIP





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



    











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%%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



    











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!chmod 755 $bashFileTmp



    











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%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

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



    











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%pushmsg "q-SIP complete: $buildDir"

delta-BD





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



    











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%%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



    











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!chmod 755 $bashFileTmp



    











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%%bash -s $workDir $bashFileTmp $buildDir
source activate py2_ley0.4
cd $1

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



    











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%pushmsg "deltaBD complete: $buildDir"

Making confusion matrices





In [53]:



    


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



    


















    
Out[53]:








'/ebio/abt3_projects/methanogen_host_evo/SIPSim_pt2/data/bac_genome1147/atomIncorp_taxaIncorp/SIPSimRun_cMtx.sh'

















In [54]:



    


%%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 (method 1: default) 
Rscript {R_dir}heavy_confuseMtx.R \
    --treat 2,4,6 \
    --con 1,3,5 \
    --method 1 \
    -o heavyM1-cMtx \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub.txt
    
# heavy-SIP (method 2) 
Rscript {R_dir}heavy_confuseMtx.R \
    --treat 2,4,6 \
    --con 1,3,5 \
    --method 2 \
    -o heavyM2-cMtx \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub.txt
    
# heavy-SIP (method 3) 
Rscript {R_dir}heavy_confuseMtx.R \
    --treat 2,4,6 \
    --con 1,3,5 \
    --method 3 \
    -o heavyM3-cMtx \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub.txt
    
# heavy-SIP (method 4) 
Rscript {R_dir}heavy_confuseMtx.R \
    --treat 2,4,6 \
    --con 1,3,5 \
    --method 4 \
    -o heavyM4-cMtx \
    BD-shift_stats.txt \
    OTU_abs{abs}_PCR_sub.txt



    


















    






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

















In [55]:



    


!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 percIncorp,percTaxa,rep \
       -o $x \
       --tab \
       $x

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

    # by class
    x = prefix + '-cMtx_byClass.txt'
    !nestagg delim \
        -d $buildDir \
        -k percIncorp,percTaxa,rep \
        -o $x \
        --tab \
        $x
        
agg_cMtx('DESeq2')
agg_cMtx('DESeq2_multi')
agg_cMtx('qSIP') 
agg_cMtx('heavyM1')
agg_cMtx('heavyM2')
agg_cMtx('heavyM3')
agg_cMtx('heavyM4')



    











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%pushmsg "atomIncorp_taxaIncorp complete!"

--End of simulation--

Results





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F = os.path.join(buildDir, '*-cMtx_byClass.txt')
files = glob.glob(F)
files



    











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



    











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Content source: nick-youngblut/SIPSim

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