Goal

Question: how does the percentage of taxa incorporating isotope affect the accuracy of DESeq2

Using genome dataset created in the "dataset" notebook
Simulates isotope dilution or short incubations
- Method
  - % of taxa w/ incorporation: 0, 5, 10, 25, 50, 75, 100
  - % isotope incorporated per taxon: 0, 20, 40, 60, 80, 100%
    - no variance on incorporation %

User variables



In [18]:

    
workDir = '/home/nick/notebook/SIPSim/dev/bac_genome1210/'
buildDir = os.path.join(workDir, 'percTaxaIncorpUnif')
genomeDir = '/home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/'
R_dir = '/home/nick/notebook/SIPSim/lib/R/'

Init



In [51]:

    
import glob
import itertools
from os.path import abspath
import nestly



In [20]:

    
%load_ext rpy2.ipython









    



The rpy2.ipython extension is already loaded. To reload it, use:
  %reload_ext rpy2.ipython



In [21]:

    
%%R
library(ggplot2)
library(dplyr)
library(tidyr)
library(gridExtra)



In [22]:

    
if not os.path.isdir(buildDir):
    os.makedirs(buildDir)

Creating input files (eg., fragments & communities)



In [ ]:

    
# 8 hour delay
!sleep 28800

Simulating fragments



In [ ]:

    
!cd $buildDir; \
    SIPSim fragments \
    $genomeDir/genome_index.txt \
    --fp $genomeDir \
    --fr ../../515F-806R.fna \
    --fld skewed-normal,9000,2500,-5 \
    --flr None,None \
    --nf 10000 \
    --np 24 \
    2> ampFrags.log \
    > ampFrags.pkl

Converting to kde object



In [ ]:

    
!cd $buildDir; \
    SIPSim fragment_kde \
    ampFrags.pkl \
    > ampFrags_kde.pkl

Adding diffusion



In [ ]:

    
!cd $buildDir; \
    SIPSim diffusion \
    ampFrags_kde.pkl \
    --np 24 \
    > ampFrags_kde_dif.pkl

Creating a community file



In [ ]:

    
!cd $buildDir; \
    SIPSim communities \
    $genomeDir/genome_index.txt \
    --n_comm 2 \
    > comm.txt

Using nestly: different incorporation percentages



In [ ]:

    
# building tree structure
nest = nestly.Nest()

## varying params
nest.add('percTaxaIncorp', [5, 10, 25, 50, 75, 100])
nest.add('percIncorp', range(0,101,25))

## set params
nest.add('np_many', [24], create_dir=False)
nest.add('np_few', [8], create_dir=False)
nest.add('abs', ['1e10'], create_dir=False)
#nest.add('subsample', [20000], create_dir=False) 
nest.add('subsample_mean', [30000], create_dir=False) 
nest.add('subsample_scale', [5000], create_dir=False) 
nest.add('BD_min', [1.71], create_dir=False)
nest.add('BD_max', [1.75], create_dir=False)
nest.add('padj', [0.1], create_dir=False)
nest.add('log2', [0.25], create_dir=False)
nest.add('topTaxaToPlot', [100], create_dir=False)

## input/output files
nest.add('buildDir', [buildDir], create_dir=False)
nest.add('frag_file', ['ampFrags_kde_dif'], create_dir=False)
nest.add('comm_file', ['comm.txt'], create_dir=False)
nest.add('genome_index', [os.path.join(genomeDir, 'genome_index.txt')], create_dir=False)
nest.add('genome_dir', [genomeDir], create_dir=False)
nest.add('primers', [os.path.join(workDir, '../', '515F-806R.fna')], create_dir=False)
nest.add('R_dir', [R_dir], create_dir=False)

# building directory tree
nest.build(buildDir)



In [ ]:

    
bashFile = os.path.join(buildDir, 'SIPSimRun.sh')



In [ ]:

    
%%writefile $bashFile
#!/bin/bash

# symlinking input files
ln -s {buildDir}/{frag_file}.pkl {frag_file}.pkl
ln -s {buildDir}/{comm_file} {comm_file}


# making incorp file
SIPSim incorpConfigExample \
  --percTaxa {percTaxaIncorp} \
  --percIncorpUnif {percIncorp} \
  > {percTaxaIncorp}_{percIncorp}.config

 
# adding isotope incorporation to BD distribution
SIPSim isotope_incorp \
    {frag_file}.pkl \
    {percTaxaIncorp}_{percIncorp}.config \
    --comm {comm_file} \
    --np {np_many} \
    > {frag_file}_incorp.pkl
     
# calculating BD shift from isotope incorporation
SIPSim BD_shift \
    {frag_file}.pkl \
    {frag_file}_incorp.pkl \
    --np {np_few} \
    > {frag_file}_incorp_BD-shift.txt
           
    
# simulating gradient fractions
SIPSim gradient_fractions \
    {comm_file} \
    > fracs.txt

# simulating an OTU table
SIPSim OTU_table \
    {frag_file}_incorp.pkl \
    {comm_file} \
    fracs.txt \
    --abs {abs} \
    --np {np_few} \
    > OTU_abs{abs}.txt
        
    
# subsampling from the OTU table (simulating sequencing of the DNA pool)
SIPSim OTU_subsample \
    --dist normal \
    --dist_params loc:{subsample_mean},scale:{subsample_scale} \
    OTU_abs{abs}.txt \
    > OTU_n2_abs{abs}_sub-norm.txt

# making a wide table
SIPSim OTU_wideLong -w \
    OTU_n2_abs{abs}_sub-norm.txt \
    > OTU_n2_abs{abs}_sub-norm_w.txt
    
# making metadata (phyloseq: sample_data)
SIPSim OTU_sampleData \
    OTU_n2_abs{abs}_sub-norm.txt \
    > OTU_n2_abs{abs}_sub-norm_meta.txt



In [ ]:

    
!chmod 775 $bashFile



In [ ]:

    
!cd $workDir; \
    nestrun -j 1 --template-file $bashFile -d percTaxaIncorpUnif --log-file log.txt









    



2015-07-18 09:11:53,426 * WARNING * [109927] percTaxaIncorpUnif/75/50 Finished with non-zero exit status 1
  File "/opt/anaconda/lib/python2.7/site-packages/pandas/io/parsers.py", line 246, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/opt/anaconda/lib/python2.7/site-packages/pandas/io/parsers.py", line 562, in __init__
    self._make_engine(self.engine)
  File "/opt/anaconda/lib/python2.7/site-packages/pandas/io/parsers.py", line 699, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "/opt/anaconda/lib/python2.7/site-packages/pandas/io/parsers.py", line 1066, in __init__
    self._reader = _parser.TextReader(src, **kwds)
  File "pandas/parser.pyx", line 512, in pandas.parser.TextReader.__cinit__ (pandas/parser.c:4804)
ValueError: No columns to parse from file

2015-07-18 09:11:53,447 * INFO * [112997] Started ./SIPSimRun.sh in percTaxaIncorpUnif/75/75
2015-07-19 07:53:39,854 * INFO * [130585] percTaxaIncorpUnif/25/25 Finished with 0
2015-07-19 07:53:39,860 * INFO * [132623] Started ./SIPSimRun.sh in percTaxaIncorpUnif/10/50

DESeq2 Analysis pipeline



In [107]:

    
buildDir_DESeq = os.path.join(buildDir, 'DESeq2')
buildDir_DESeq









    Out[107]:





'/home/nick/notebook/SIPSim/dev/bac_genome1210/percTaxaIncorpUnif/DESeq2'



In [108]:

    
# building tree structure
nest = nestly.Nest()

## varying params
nest.add('percTaxaIncorp', [5, 10, 25, 50, 75, 100])
nest.add('percIncorp', range(0,101,25))
### BD range
BD_min = np.arange(1.67, 1.77, 0.02).tolist()
BD_max = [x + 0.04 for x in BD_min]
f = lambda x: {'BD_range': str(x[0]) + '-' + str(x[1]), 
               'BD_min':x[0], 
               'BD_max':x[1]}
BD_range = [f(x) for x in itertools.product(BD_min, BD_max) 
            if x[0] < x[1]]
#### contains BD_min & BD_max
nest.add('BD_range', BD_range, update=True)

## set params
nest.add('np_many', [24], create_dir=False)
nest.add('np_few', [8], create_dir=False)
nest.add('abs', ['1e10'], create_dir=False)
#nest.add('subsample', [20000], create_dir=False) 
nest.add('subsample_mean', [30000], create_dir=False) 
nest.add('subsample_scale', [5000], create_dir=False) 
nest.add('padj', [0.1], create_dir=False)
nest.add('log2', [0.25], create_dir=False)
nest.add('topTaxaToPlot', [100], create_dir=False)

## input/output files
nest.add('buildDir', [buildDir], create_dir=False)
nest.add('frag_file', ['ampFrags_kde_dif'], create_dir=False)
nest.add('comm_file', ['comm.txt'], create_dir=False)
nest.add('genome_index', [os.path.join(genomeDir, 'genome_index.txt')], create_dir=False)
nest.add('genome_dir', [genomeDir], create_dir=False)
nest.add('primers', [os.path.join(workDir, '../', '515F-806R.fna')], create_dir=False)
nest.add('R_dir', [R_dir], create_dir=False)

# building directory tree
nest.build(buildDir_DESeq)



In [109]:

    
%%writefile $bashFile
#!/bin/bash

# copying all input files
cp {buildDir}/{percTaxaIncorp}/{percIncorp}/OTU_n2_abs{abs}_sub-norm.txt OTU_n2_abs{abs}_sub-norm.txt
cp {buildDir}/{percTaxaIncorp}/{percIncorp}/OTU_n2_abs{abs}_sub-norm_w.txt OTU_n2_abs{abs}_sub-norm_w.txt
cp {buildDir}/{percTaxaIncorp}/{percIncorp}/OTU_n2_abs{abs}_sub-norm_meta.txt OTU_n2_abs{abs}_sub-norm_meta.txt
cp {buildDir}/{percTaxaIncorp}/{percIncorp}/{frag_file}_incorp_BD-shift.txt {frag_file}_incorp_BD-shift.txt


#-- R analysis --#
export PATH={R_dir}:$PATH
# plotting taxon abundances
OTU_taxonAbund.r \
    OTU_n2_abs{abs}_sub-norm.txt \
    -r {topTaxaToPlot} \
    -o OTU_n2_abs{abs}_subsub-norm
# running DeSeq2 and making confusion matrix on predicting incorporators
## making phyloseq object from OTU table
phyloseq_make.r \
    OTU_n2_abs{abs}_sub-norm_w.txt \
    -s OTU_n2_abs{abs}_sub-norm_meta.txt \
    > OTU_n2_abs{abs}_sub-norm.physeq
## filtering phyloseq object to just taxa/samples of interest
phyloseq_edit.r \
    OTU_n2_abs{abs}_sub-norm.physeq \
    --BD_min {BD_min} \
    --BD_max {BD_max} \
    > OTU_n2_abs{abs}_sub-norm_filt.physeq
## making ordination
#phyloseq_ordination.r \
#    OTU_n2_abs{abs}_sub-norm_filt.physeq \
#    OTU_n2_abs{abs}_sub-norm_bray-NMDS.pdf
## DESeq2
phyloseq_DESeq2.r \
    OTU_n2_abs{abs}_sub-norm_filt.physeq \
    --log2 {log2} \
    --hypo greater \
    > OTU_n2_abs{abs}_sub-norm_DESeq2
## Confusion matrix
DESeq2_confuseMtx.r \
    {frag_file}_incorp_BD-shift.txt \
    OTU_n2_abs{abs}_sub-norm_DESeq2 \
    --padj {padj}









    



Overwriting /home/nick/notebook/SIPSim/dev/bac_genome1210/percTaxaIncorpUnif/SIPSimRun.sh



In [113]:

    
%%R -i buildDir
# debug
setwd(buildDir)

physeq = readRDS('50/75/1.69-1.77/OTU_n2_abs1e10_sub-norm.physeq')









    



Error in opts[["<phyloseq>"]] : 
  object of type 'closure' is not subsettable



In [110]:

    
!chmod 775 $bashFile



In [111]:

    
!cd $workDir; \
    nestrun -j 30 --template-file $bashFile -d percTaxaIncorpUnif/DESeq2 --log-file log.txt









    



2015-07-20 09:18:03,102 * INFO * Template: ./SIPSimRun.sh
2015-07-20 09:18:03,104 * INFO * [198282] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.67-1.79
2015-07-20 09:18:03,107 * INFO * [198283] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.73-1.77
2015-07-20 09:18:03,109 * INFO * [198285] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.69-1.77
2015-07-20 09:18:03,111 * INFO * [198288] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.71-1.75
2015-07-20 09:18:03,113 * INFO * [198290] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.75-1.81
2015-07-20 09:18:03,116 * INFO * [198293] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.71-1.73
2015-07-20 09:18:03,118 * INFO * [198298] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.73-1.79
2015-07-20 09:18:03,119 * INFO * [198303] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.69-1.71
2015-07-20 09:18:03,121 * INFO * [198311] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.77-1.81
2015-07-20 09:18:03,123 * INFO * [198316] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.69-1.73
2015-07-20 09:18:03,125 * INFO * [198332] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.69-1.79
2015-07-20 09:18:03,128 * INFO * [198347] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.67-1.77
2015-07-20 09:18:03,130 * INFO * [198355] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.75-1.79
2015-07-20 09:18:03,132 * INFO * [198366] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.69-1.75
2015-07-20 09:18:03,133 * INFO * [198382] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.67-1.75
2015-07-20 09:18:03,135 * INFO * [198395] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.75-1.77
2015-07-20 09:18:03,137 * INFO * [198404] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.67-1.81
2015-07-20 09:18:03,138 * INFO * [198416] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.73-1.75
2015-07-20 09:18:03,140 * INFO * [198429] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.71-1.77
2015-07-20 09:18:03,143 * INFO * [198439] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.69-1.81
2015-07-20 09:18:03,145 * INFO * [198444] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.67-1.71
2015-07-20 09:18:03,146 * INFO * [198461] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.73-1.81
2015-07-20 09:18:03,148 * INFO * [198469] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.71-1.81
2015-07-20 09:18:03,150 * INFO * [198479] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.71-1.79
2015-07-20 09:18:03,153 * INFO * [198494] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.67-1.73
2015-07-20 09:18:03,156 * INFO * [198507] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/50/1.77-1.79
2015-07-20 09:18:03,158 * INFO * [198517] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.67-1.79
2015-07-20 09:18:03,160 * INFO * [198523] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.73-1.77
2015-07-20 09:18:03,162 * INFO * [198537] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.69-1.77
2015-07-20 09:18:03,164 * INFO * [198547] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.71-1.75
2015-07-20 09:19:07,031 * WARNING * [198537] percTaxaIncorpUnif/DESeq2/50/75/1.69-1.77 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:19:07,033 * INFO * [200289] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.75-1.81
2015-07-20 09:19:10,128 * INFO * [198469] percTaxaIncorpUnif/DESeq2/50/50/1.71-1.81 Finished with 0
2015-07-20 09:19:10,130 * INFO * [200341] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.71-1.73
2015-07-20 09:19:10,451 * WARNING * [198547] percTaxaIncorpUnif/DESeq2/50/75/1.71-1.75 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:19:10,454 * INFO * [200355] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.73-1.79
2015-07-20 09:19:10,498 * INFO * [198395] percTaxaIncorpUnif/DESeq2/50/50/1.75-1.77 Finished with 0
2015-07-20 09:19:10,501 * INFO * [200367] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.69-1.71
2015-07-20 09:19:11,098 * WARNING * [198523] percTaxaIncorpUnif/DESeq2/50/75/1.73-1.77 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:19:11,100 * INFO * [200392] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.77-1.81
2015-07-20 09:19:11,491 * INFO * [198439] percTaxaIncorpUnif/DESeq2/50/50/1.69-1.81 Finished with 0
2015-07-20 09:19:11,493 * INFO * [200417] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.69-1.73
2015-07-20 09:19:11,899 * INFO * [198298] percTaxaIncorpUnif/DESeq2/50/50/1.73-1.79 Finished with 0
2015-07-20 09:19:11,901 * INFO * [200436] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.69-1.79
2015-07-20 09:19:12,065 * INFO * [198288] percTaxaIncorpUnif/DESeq2/50/50/1.71-1.75 Finished with 0
2015-07-20 09:19:12,068 * INFO * [200461] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.67-1.77
2015-07-20 09:19:12,910 * INFO * [198293] percTaxaIncorpUnif/DESeq2/50/50/1.71-1.73 Finished with 0
2015-07-20 09:19:12,912 * INFO * [200500] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.75-1.79
2015-07-20 09:19:13,059 * INFO * [198285] percTaxaIncorpUnif/DESeq2/50/50/1.69-1.77 Finished with 0
2015-07-20 09:19:13,061 * INFO * [200513] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.69-1.75
2015-07-20 09:19:13,449 * INFO * [198366] percTaxaIncorpUnif/DESeq2/50/50/1.69-1.75 Finished with 0
2015-07-20 09:19:13,452 * INFO * [200532] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.67-1.75
2015-07-20 09:19:13,928 * INFO * [198382] percTaxaIncorpUnif/DESeq2/50/50/1.67-1.75 Finished with 0
2015-07-20 09:19:13,930 * INFO * [200554] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.75-1.77
2015-07-20 09:19:13,936 * WARNING * [198517] percTaxaIncorpUnif/DESeq2/50/75/1.67-1.79 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:19:13,939 * INFO * [200558] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.67-1.81
2015-07-20 09:19:13,961 * INFO * [198311] percTaxaIncorpUnif/DESeq2/50/50/1.77-1.81 Finished with 0
2015-07-20 09:19:13,963 * INFO * [200577] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.73-1.75
2015-07-20 09:19:14,079 * INFO * [198332] percTaxaIncorpUnif/DESeq2/50/50/1.69-1.79 Finished with 0
2015-07-20 09:19:14,081 * INFO * [200590] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.71-1.77
2015-07-20 09:19:14,553 * INFO * [198507] percTaxaIncorpUnif/DESeq2/50/50/1.77-1.79 Finished with 0
2015-07-20 09:19:14,556 * INFO * [200609] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.69-1.81
2015-07-20 09:19:14,649 * INFO * [198479] percTaxaIncorpUnif/DESeq2/50/50/1.71-1.79 Finished with 0
2015-07-20 09:19:14,652 * INFO * [200630] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.67-1.71
2015-07-20 09:19:14,678 * INFO * [198290] percTaxaIncorpUnif/DESeq2/50/50/1.75-1.81 Finished with 0
2015-07-20 09:19:14,680 * INFO * [200641] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.73-1.81
2015-07-20 09:19:15,159 * INFO * [198416] percTaxaIncorpUnif/DESeq2/50/50/1.73-1.75 Finished with 0
2015-07-20 09:19:15,162 * INFO * [200660] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.71-1.81
2015-07-20 09:19:15,596 * INFO * [198461] percTaxaIncorpUnif/DESeq2/50/50/1.73-1.81 Finished with 0
2015-07-20 09:19:15,600 * INFO * [200681] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.71-1.79
2015-07-20 09:19:15,995 * INFO * [198316] percTaxaIncorpUnif/DESeq2/50/50/1.69-1.73 Finished with 0
2015-07-20 09:19:15,997 * INFO * [200700] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.67-1.73
2015-07-20 09:19:16,139 * INFO * [198429] percTaxaIncorpUnif/DESeq2/50/50/1.71-1.77 Finished with 0
2015-07-20 09:19:16,141 * INFO * [200719] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/75/1.77-1.79
2015-07-20 09:19:16,676 * INFO * [198494] percTaxaIncorpUnif/DESeq2/50/50/1.67-1.73 Finished with 0
2015-07-20 09:19:16,678 * INFO * [200738] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.67-1.79
2015-07-20 09:19:17,129 * INFO * [198283] percTaxaIncorpUnif/DESeq2/50/50/1.73-1.77 Finished with 0
2015-07-20 09:19:17,132 * INFO * [200767] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.73-1.77
2015-07-20 09:19:17,776 * INFO * [198347] percTaxaIncorpUnif/DESeq2/50/50/1.67-1.77 Finished with 0
2015-07-20 09:19:17,778 * INFO * [200788] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.69-1.77
2015-07-20 09:19:18,170 * INFO * [198444] percTaxaIncorpUnif/DESeq2/50/50/1.67-1.71 Finished with 0
2015-07-20 09:19:18,173 * INFO * [200817] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.71-1.75
2015-07-20 09:19:18,608 * INFO * [198355] percTaxaIncorpUnif/DESeq2/50/50/1.75-1.79 Finished with 0
2015-07-20 09:19:18,611 * INFO * [200850] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.75-1.81
2015-07-20 09:19:19,975 * INFO * [198404] percTaxaIncorpUnif/DESeq2/50/50/1.67-1.81 Finished with 0
2015-07-20 09:19:19,977 * INFO * [200912] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.71-1.73
2015-07-20 09:19:20,957 * INFO * [198303] percTaxaIncorpUnif/DESeq2/50/50/1.69-1.71 Finished with 0
2015-07-20 09:19:20,960 * INFO * [200972] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.73-1.79
2015-07-20 09:19:22,428 * INFO * [198282] percTaxaIncorpUnif/DESeq2/50/50/1.67-1.79 Finished with 0
2015-07-20 09:19:22,430 * INFO * [201045] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.69-1.71
2015-07-20 09:20:07,010 * WARNING * [200289] percTaxaIncorpUnif/DESeq2/50/75/1.75-1.81 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:07,012 * INFO * [202195] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.77-1.81
2015-07-20 09:20:10,026 * WARNING * [200355] percTaxaIncorpUnif/DESeq2/50/75/1.73-1.79 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:10,029 * INFO * [202302] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.69-1.73
2015-07-20 09:20:11,634 * WARNING * [200392] percTaxaIncorpUnif/DESeq2/50/75/1.77-1.81 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:11,637 * INFO * [202367] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.69-1.79
2015-07-20 09:20:12,666 * WARNING * [200558] percTaxaIncorpUnif/DESeq2/50/75/1.67-1.81 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:12,669 * INFO * [202396] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.67-1.77
2015-07-20 09:20:12,696 * WARNING * [200341] percTaxaIncorpUnif/DESeq2/50/75/1.71-1.73 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:12,699 * INFO * [202409] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.75-1.79
2015-07-20 09:20:13,940 * WARNING * [200367] percTaxaIncorpUnif/DESeq2/50/75/1.69-1.71 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:13,942 * INFO * [202446] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.69-1.75
2015-07-20 09:20:14,035 * WARNING * [200417] percTaxaIncorpUnif/DESeq2/50/75/1.69-1.73 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:14,037 * INFO * [202465] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.67-1.75
2015-07-20 09:20:14,629 * WARNING * [200513] percTaxaIncorpUnif/DESeq2/50/75/1.69-1.75 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:14,631 * INFO * [202478] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.75-1.77
2015-07-20 09:20:14,946 * WARNING * [200577] percTaxaIncorpUnif/DESeq2/50/75/1.73-1.75 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:14,949 * INFO * [202491] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.67-1.81
2015-07-20 09:20:15,153 * WARNING * [200554] percTaxaIncorpUnif/DESeq2/50/75/1.75-1.77 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:15,155 * INFO * [202516] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.73-1.75
2015-07-20 09:20:15,284 * WARNING * [200436] percTaxaIncorpUnif/DESeq2/50/75/1.69-1.79 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:15,286 * INFO * [202539] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.71-1.77
2015-07-20 09:20:15,317 * WARNING * [200590] percTaxaIncorpUnif/DESeq2/50/75/1.71-1.77 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:15,319 * INFO * [202558] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.69-1.81
2015-07-20 09:20:16,244 * WARNING * [200660] percTaxaIncorpUnif/DESeq2/50/75/1.71-1.81 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:16,247 * INFO * [202619] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.67-1.71
2015-07-20 09:20:16,634 * WARNING * [200500] percTaxaIncorpUnif/DESeq2/50/75/1.75-1.79 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:16,637 * INFO * [202632] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.73-1.81
2015-07-20 09:20:18,226 * WARNING * [200719] percTaxaIncorpUnif/DESeq2/50/75/1.77-1.79 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:18,229 * INFO * [202719] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.71-1.81
2015-07-20 09:20:19,090 * WARNING * [200700] percTaxaIncorpUnif/DESeq2/50/75/1.67-1.73 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:19,093 * INFO * [202773] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.71-1.79
2015-07-20 09:20:19,318 * WARNING * [200630] percTaxaIncorpUnif/DESeq2/50/75/1.67-1.71 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:19,321 * INFO * [202786] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.67-1.73
2015-07-20 09:20:20,276 * WARNING * [200641] percTaxaIncorpUnif/DESeq2/50/75/1.73-1.81 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:20,278 * INFO * [202799] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/0/1.77-1.79
2015-07-20 09:20:20,642 * WARNING * [200461] percTaxaIncorpUnif/DESeq2/50/75/1.67-1.77 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:20,645 * INFO * [202822] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.67-1.79
2015-07-20 09:20:22,400 * WARNING * [200609] percTaxaIncorpUnif/DESeq2/50/75/1.69-1.81 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:22,403 * INFO * [202883] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.73-1.77
2015-07-20 09:20:22,716 * INFO * [200912] percTaxaIncorpUnif/DESeq2/50/0/1.71-1.73 Finished with 0
2015-07-20 09:20:22,719 * INFO * [202910] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.69-1.77
2015-07-20 09:20:23,783 * WARNING * [200532] percTaxaIncorpUnif/DESeq2/50/75/1.67-1.75 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:23,787 * INFO * [202925] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.71-1.75
2015-07-20 09:20:25,828 * WARNING * [200681] percTaxaIncorpUnif/DESeq2/50/75/1.71-1.79 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:20:25,830 * INFO * [202970] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.75-1.81
2015-07-20 09:20:30,390 * INFO * [200767] percTaxaIncorpUnif/DESeq2/50/0/1.73-1.77 Finished with 0
2015-07-20 09:20:30,393 * INFO * [203093] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.71-1.73
2015-07-20 09:20:32,150 * INFO * [200788] percTaxaIncorpUnif/DESeq2/50/0/1.69-1.77 Finished with 0
2015-07-20 09:20:32,153 * INFO * [203176] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.73-1.79
2015-07-20 09:20:33,515 * INFO * [200817] percTaxaIncorpUnif/DESeq2/50/0/1.71-1.75 Finished with 0
2015-07-20 09:20:33,518 * INFO * [203221] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.69-1.71
2015-07-20 09:20:33,643 * INFO * [201045] percTaxaIncorpUnif/DESeq2/50/0/1.69-1.71 Finished with 0
2015-07-20 09:20:33,646 * INFO * [203234] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.77-1.81
2015-07-20 09:20:34,609 * INFO * [200972] percTaxaIncorpUnif/DESeq2/50/0/1.73-1.79 Finished with 0
2015-07-20 09:20:34,612 * INFO * [203287] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.69-1.73
2015-07-20 09:20:36,293 * INFO * [200738] percTaxaIncorpUnif/DESeq2/50/0/1.67-1.79 Finished with 0
2015-07-20 09:20:36,295 * INFO * [203340] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.69-1.79
2015-07-20 09:20:36,788 * INFO * [200850] percTaxaIncorpUnif/DESeq2/50/0/1.75-1.81 Finished with 0
2015-07-20 09:20:36,790 * INFO * [203379] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.67-1.77
2015-07-20 09:21:18,706 * INFO * [202195] percTaxaIncorpUnif/DESeq2/50/0/1.77-1.81 Finished with 0
2015-07-20 09:21:18,709 * INFO * [204448] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.75-1.79
2015-07-20 09:21:21,967 * INFO * [202302] percTaxaIncorpUnif/DESeq2/50/0/1.69-1.73 Finished with 0
2015-07-20 09:21:21,970 * INFO * [204505] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.69-1.75
2015-07-20 09:21:23,157 * INFO * [202409] percTaxaIncorpUnif/DESeq2/50/0/1.75-1.79 Finished with 0
2015-07-20 09:21:23,159 * INFO * [204537] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.67-1.75
2015-07-20 09:21:23,210 * INFO * [202478] percTaxaIncorpUnif/DESeq2/50/0/1.75-1.77 Finished with 0
2015-07-20 09:21:23,213 * INFO * [204549] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.75-1.77
2015-07-20 09:21:24,354 * INFO * [202773] percTaxaIncorpUnif/DESeq2/50/0/1.71-1.79 Finished with 0
2015-07-20 09:21:24,356 * INFO * [204610] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.67-1.81
2015-07-20 09:21:24,726 * INFO * [202632] percTaxaIncorpUnif/DESeq2/50/0/1.73-1.81 Finished with 0
2015-07-20 09:21:24,728 * INFO * [204635] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.73-1.75
2015-07-20 09:21:24,849 * INFO * [202516] percTaxaIncorpUnif/DESeq2/50/0/1.73-1.75 Finished with 0
2015-07-20 09:21:24,852 * INFO * [204648] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.71-1.77
2015-07-20 09:21:26,292 * INFO * [202465] percTaxaIncorpUnif/DESeq2/50/0/1.67-1.75 Finished with 0
2015-07-20 09:21:26,294 * INFO * [204681] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.69-1.81
2015-07-20 09:21:26,460 * INFO * [202367] percTaxaIncorpUnif/DESeq2/50/0/1.69-1.79 Finished with 0
2015-07-20 09:21:26,463 * INFO * [204702] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.67-1.71
2015-07-20 09:21:27,069 * INFO * [202491] percTaxaIncorpUnif/DESeq2/50/0/1.67-1.81 Finished with 0
2015-07-20 09:21:27,072 * INFO * [204727] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.73-1.81
2015-07-20 09:21:29,150 * INFO * [202539] percTaxaIncorpUnif/DESeq2/50/0/1.71-1.77 Finished with 0
2015-07-20 09:21:29,153 * INFO * [204774] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.71-1.81
2015-07-20 09:21:30,079 * INFO * [202619] percTaxaIncorpUnif/DESeq2/50/0/1.67-1.71 Finished with 0
2015-07-20 09:21:30,081 * INFO * [204807] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.71-1.79
2015-07-20 09:21:30,841 * INFO * [202446] percTaxaIncorpUnif/DESeq2/50/0/1.69-1.75 Finished with 0
2015-07-20 09:21:30,844 * INFO * [204836] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.67-1.73
2015-07-20 09:21:31,167 * INFO * [202558] percTaxaIncorpUnif/DESeq2/50/0/1.69-1.81 Finished with 0
2015-07-20 09:21:31,170 * INFO * [204869] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/100/1.77-1.79
2015-07-20 09:21:31,999 * WARNING * [203234] percTaxaIncorpUnif/DESeq2/50/100/1.77-1.81 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:21:32,002 * INFO * [204888] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.67-1.79
2015-07-20 09:21:32,105 * INFO * [202396] percTaxaIncorpUnif/DESeq2/50/0/1.67-1.77 Finished with 0
2015-07-20 09:21:32,107 * INFO * [204901] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.73-1.77
2015-07-20 09:21:32,288 * INFO * [202799] percTaxaIncorpUnif/DESeq2/50/0/1.77-1.79 Finished with 0
2015-07-20 09:21:32,290 * INFO * [204922] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.69-1.77
2015-07-20 09:21:33,181 * INFO * [202822] percTaxaIncorpUnif/DESeq2/50/100/1.67-1.79 Finished with 0
2015-07-20 09:21:33,184 * INFO * [204967] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.71-1.75
2015-07-20 09:21:34,386 * INFO * [202719] percTaxaIncorpUnif/DESeq2/50/0/1.71-1.81 Finished with 0
2015-07-20 09:21:34,389 * INFO * [205004] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.75-1.81
2015-07-20 09:21:35,591 * INFO * [202786] percTaxaIncorpUnif/DESeq2/50/0/1.67-1.73 Finished with 0
2015-07-20 09:21:35,594 * INFO * [205057] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.71-1.73
2015-07-20 09:21:35,651 * INFO * [202910] percTaxaIncorpUnif/DESeq2/50/100/1.69-1.77 Finished with 0
2015-07-20 09:21:35,653 * INFO * [205070] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.73-1.79
2015-07-20 09:21:37,134 * INFO * [202925] percTaxaIncorpUnif/DESeq2/50/100/1.71-1.75 Finished with 0
2015-07-20 09:21:37,136 * INFO * [205119] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.69-1.71
2015-07-20 09:21:37,379 * INFO * [202970] percTaxaIncorpUnif/DESeq2/50/100/1.75-1.81 Finished with 0
2015-07-20 09:21:37,382 * INFO * [205132] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.77-1.81
2015-07-20 09:21:37,863 * WARNING * [203221] percTaxaIncorpUnif/DESeq2/50/100/1.69-1.71 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:21:37,866 * INFO * [205145] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.69-1.73
2015-07-20 09:21:39,420 * INFO * [202883] percTaxaIncorpUnif/DESeq2/50/100/1.73-1.77 Finished with 0
2015-07-20 09:21:39,423 * INFO * [205198] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.69-1.79
2015-07-20 09:21:48,216 * INFO * [203287] percTaxaIncorpUnif/DESeq2/50/100/1.69-1.73 Finished with 0
2015-07-20 09:21:48,219 * INFO * [205436] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.67-1.77
2015-07-20 09:21:48,568 * INFO * [203340] percTaxaIncorpUnif/DESeq2/50/100/1.69-1.79 Finished with 0
2015-07-20 09:21:48,570 * INFO * [205458] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.75-1.79
2015-07-20 09:21:50,864 * INFO * [203093] percTaxaIncorpUnif/DESeq2/50/100/1.71-1.73 Finished with 0
2015-07-20 09:21:50,867 * INFO * [205501] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.69-1.75
2015-07-20 09:21:52,159 * INFO * [203176] percTaxaIncorpUnif/DESeq2/50/100/1.73-1.79 Finished with 0
2015-07-20 09:21:52,162 * INFO * [205572] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.67-1.75
2015-07-20 09:21:56,167 * INFO * [203379] percTaxaIncorpUnif/DESeq2/50/100/1.67-1.77 Finished with 0
2015-07-20 09:21:56,171 * INFO * [205693] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.75-1.77
2015-07-20 09:22:27,795 * WARNING * [204635] percTaxaIncorpUnif/DESeq2/50/100/1.73-1.75 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:22:27,797 * INFO * [206520] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.67-1.81
2015-07-20 09:22:30,627 * WARNING * [204702] percTaxaIncorpUnif/DESeq2/50/100/1.67-1.71 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:22:30,630 * INFO * [206606] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.73-1.75
2015-07-20 09:22:35,139 * WARNING * [204901] percTaxaIncorpUnif/DESeq2/50/25/1.73-1.77 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:22:35,141 * INFO * [206717] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.71-1.77
2015-07-20 09:22:35,803 * INFO * [204681] percTaxaIncorpUnif/DESeq2/50/100/1.69-1.81 Finished with 0
2015-07-20 09:22:35,805 * INFO * [206758] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.69-1.81
2015-07-20 09:22:35,942 * INFO * [204505] percTaxaIncorpUnif/DESeq2/50/100/1.69-1.75 Finished with 0
2015-07-20 09:22:35,945 * INFO * [206776] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.67-1.71
2015-07-20 09:22:37,343 * WARNING * [204869] percTaxaIncorpUnif/DESeq2/50/100/1.77-1.79 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:22:37,345 * INFO * [206818] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.73-1.81
2015-07-20 09:22:37,641 * INFO * [204537] percTaxaIncorpUnif/DESeq2/50/100/1.67-1.75 Finished with 0
2015-07-20 09:22:37,644 * INFO * [206837] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.71-1.81
2015-07-20 09:22:37,958 * INFO * [204549] percTaxaIncorpUnif/DESeq2/50/100/1.75-1.77 Finished with 0
2015-07-20 09:22:37,960 * INFO * [206850] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.71-1.79
2015-07-20 09:22:38,677 * WARNING * [205004] percTaxaIncorpUnif/DESeq2/50/25/1.75-1.81 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:22:38,680 * INFO * [206895] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.67-1.73
2015-07-20 09:22:39,337 * INFO * [204774] percTaxaIncorpUnif/DESeq2/50/100/1.71-1.81 Finished with 0
2015-07-20 09:22:39,340 * INFO * [206926] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/50/25/1.77-1.79
2015-07-20 09:22:40,091 * INFO * [204448] percTaxaIncorpUnif/DESeq2/50/100/1.75-1.79 Finished with 0
2015-07-20 09:22:40,095 * INFO * [206945] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.67-1.79
2015-07-20 09:22:41,251 * WARNING * [205070] percTaxaIncorpUnif/DESeq2/50/25/1.73-1.79 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:22:41,254 * INFO * [206986] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.73-1.77
2015-07-20 09:22:41,276 * WARNING * [205119] percTaxaIncorpUnif/DESeq2/50/25/1.69-1.71 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:22:41,279 * INFO * [206998] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.69-1.77
2015-07-20 09:22:41,573 * INFO * [204610] percTaxaIncorpUnif/DESeq2/50/100/1.67-1.81 Finished with 0
2015-07-20 09:22:41,580 * INFO * [207012] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.71-1.75
2015-07-20 09:22:41,735 * WARNING * [205132] percTaxaIncorpUnif/DESeq2/50/25/1.77-1.81 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:22:41,738 * INFO * [207025] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.75-1.81
2015-07-20 09:22:42,837 * INFO * [204648] percTaxaIncorpUnif/DESeq2/50/100/1.71-1.77 Finished with 0
2015-07-20 09:22:42,839 * INFO * [207052] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.71-1.73
2015-07-20 09:22:43,269 * INFO * [204807] percTaxaIncorpUnif/DESeq2/50/100/1.71-1.79 Finished with 0
2015-07-20 09:22:43,272 * INFO * [207076] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.73-1.79
2015-07-20 09:22:44,346 * INFO * [204967] percTaxaIncorpUnif/DESeq2/50/25/1.71-1.75 Finished with 0
2015-07-20 09:22:44,349 * INFO * [207116] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.69-1.71
2015-07-20 09:22:45,342 * INFO * [204727] percTaxaIncorpUnif/DESeq2/50/100/1.73-1.81 Finished with 0
2015-07-20 09:22:45,344 * INFO * [207159] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.77-1.81
2015-07-20 09:22:47,333 * INFO * [204922] percTaxaIncorpUnif/DESeq2/50/25/1.69-1.77 Finished with 0
2015-07-20 09:22:47,335 * INFO * [207210] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.69-1.73
2015-07-20 09:22:48,561 * INFO * [204836] percTaxaIncorpUnif/DESeq2/50/100/1.67-1.73 Finished with 0
2015-07-20 09:22:48,564 * INFO * [207245] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.69-1.79
2015-07-20 09:22:49,891 * INFO * [205057] percTaxaIncorpUnif/DESeq2/50/25/1.71-1.73 Finished with 0
2015-07-20 09:22:49,893 * INFO * [207314] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.67-1.77
2015-07-20 09:22:51,233 * WARNING * [205458] percTaxaIncorpUnif/DESeq2/50/25/1.75-1.79 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:22:51,235 * INFO * [207365] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.75-1.79
2015-07-20 09:22:51,617 * INFO * [205198] percTaxaIncorpUnif/DESeq2/50/25/1.69-1.79 Finished with 0
2015-07-20 09:22:51,620 * INFO * [207379] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.69-1.75
2015-07-20 09:22:51,665 * INFO * [204888] percTaxaIncorpUnif/DESeq2/50/25/1.67-1.79 Finished with 0
2015-07-20 09:22:51,669 * INFO * [207391] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.67-1.75
2015-07-20 09:22:56,307 * INFO * [205145] percTaxaIncorpUnif/DESeq2/50/25/1.69-1.73 Finished with 0
2015-07-20 09:22:56,310 * INFO * [207482] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.75-1.77
2015-07-20 09:22:59,953 * INFO * [205501] percTaxaIncorpUnif/DESeq2/50/25/1.69-1.75 Finished with 0
2015-07-20 09:22:59,955 * INFO * [207627] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.67-1.81
2015-07-20 09:23:04,231 * WARNING * [205693] percTaxaIncorpUnif/DESeq2/50/25/1.75-1.77 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:23:04,234 * INFO * [207742] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.73-1.75
2015-07-20 09:23:04,318 * INFO * [205436] percTaxaIncorpUnif/DESeq2/50/25/1.67-1.77 Finished with 0
2015-07-20 09:23:04,321 * INFO * [207757] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.71-1.77
2015-07-20 09:23:08,339 * INFO * [205572] percTaxaIncorpUnif/DESeq2/50/25/1.67-1.75 Finished with 0
2015-07-20 09:23:08,341 * INFO * [207874] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.69-1.81
2015-07-20 09:23:33,083 * WARNING * [206606] percTaxaIncorpUnif/DESeq2/50/25/1.73-1.75 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:23:33,085 * INFO * [208535] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.67-1.71
2015-07-20 09:23:36,813 * WARNING * [206776] percTaxaIncorpUnif/DESeq2/50/25/1.67-1.71 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:23:36,816 * INFO * [208636] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.73-1.81
2015-07-20 09:23:37,331 * WARNING * [206818] percTaxaIncorpUnif/DESeq2/50/25/1.73-1.81 Finished with non-zero exit status 1
all genes have equal values for all samples. will not be able to perform differential analysis
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: phyloseq_to_deseq2 ... model.matrix -> model.matrix.default -> contrasts<-
In addition: Warning message:
In DESeqDataSet(se, design = design, ignoreRank) :
  some variables in design formula are characters, converting to factors
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:23:37,333 * INFO * [208649] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.71-1.81
2015-07-20 09:23:37,784 * WARNING * [206926] percTaxaIncorpUnif/DESeq2/50/25/1.77-1.79 Finished with non-zero exit status 1
File written: OTU_n2_abs1e10_subsub-norm_abs-abund.pdf
File written: OTU_n2_abs1e10_subsub-norm_rel-abund.pdf
Error in validObject(.Object) : invalid class “otu_table” object: 
 OTU abundance data must have non-zero dimensions.
Calls: prune_samples ... .nextMethod -> callNextMethod -> .nextMethod -> validObject
Execution halted
Error in readRDS(opts[["<phyloseq>"]]) : error reading from connection
Execution halted
Error in readRDS(opts[["<DESeq2>"]]) : error reading from connection
Execution halted

2015-07-20 09:23:37,786 * INFO * [208672] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.71-1.79
2015-07-20 09:23:40,894 * INFO * [206520] percTaxaIncorpUnif/DESeq2/50/25/1.67-1.81 Finished with 0
2015-07-20 09:23:40,897 * INFO * [208759] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.67-1.73
2015-07-20 09:23:41,039 * INFO * [206758] percTaxaIncorpUnif/DESeq2/50/25/1.69-1.81 Finished with 0
2015-07-20 09:23:41,041 * INFO * [208772] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/50/1.77-1.79
2015-07-20 09:23:49,789 * INFO * [206717] percTaxaIncorpUnif/DESeq2/50/25/1.71-1.77 Finished with 0
2015-07-20 09:23:49,792 * INFO * [208988] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.67-1.79
2015-07-20 09:23:52,756 * INFO * [206850] percTaxaIncorpUnif/DESeq2/50/25/1.71-1.79 Finished with 0
2015-07-20 09:23:52,758 * INFO * [209051] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.73-1.77
2015-07-20 09:23:54,115 * INFO * [207025] percTaxaIncorpUnif/DESeq2/75/50/1.75-1.81 Finished with 0
2015-07-20 09:23:54,118 * INFO * [209102] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.69-1.77
2015-07-20 09:23:54,164 * INFO * [206837] percTaxaIncorpUnif/DESeq2/50/25/1.71-1.81 Finished with 0
2015-07-20 09:23:54,166 * INFO * [209119] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.71-1.75
2015-07-20 09:23:57,130 * INFO * [206998] percTaxaIncorpUnif/DESeq2/75/50/1.69-1.77 Finished with 0
2015-07-20 09:23:57,132 * INFO * [209202] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.75-1.81
2015-07-20 09:23:58,704 * INFO * [207159] percTaxaIncorpUnif/DESeq2/75/50/1.77-1.81 Finished with 0
2015-07-20 09:23:58,706 * INFO * [209263] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.71-1.73
2015-07-20 09:23:59,101 * INFO * [207052] percTaxaIncorpUnif/DESeq2/75/50/1.71-1.73 Finished with 0
2015-07-20 09:23:59,104 * INFO * [209298] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.73-1.79
2015-07-20 09:24:01,172 * INFO * [206895] percTaxaIncorpUnif/DESeq2/50/25/1.67-1.73 Finished with 0
2015-07-20 09:24:01,175 * INFO * [209359] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.69-1.71
2015-07-20 09:24:01,438 * INFO * [206945] percTaxaIncorpUnif/DESeq2/75/50/1.67-1.79 Finished with 0
2015-07-20 09:24:01,441 * INFO * [209372] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.77-1.81
2015-07-20 09:24:01,874 * INFO * [207116] percTaxaIncorpUnif/DESeq2/75/50/1.69-1.71 Finished with 0
2015-07-20 09:24:01,877 * INFO * [209393] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.69-1.73
2015-07-20 09:24:02,377 * INFO * [207012] percTaxaIncorpUnif/DESeq2/75/50/1.71-1.75 Finished with 0
2015-07-20 09:24:02,380 * INFO * [209406] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.69-1.79
2015-07-20 09:24:03,090 * INFO * [207210] percTaxaIncorpUnif/DESeq2/75/50/1.69-1.73 Finished with 0
2015-07-20 09:24:03,093 * INFO * [209431] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.67-1.77
2015-07-20 09:24:05,077 * INFO * [206986] percTaxaIncorpUnif/DESeq2/75/50/1.73-1.77 Finished with 0
2015-07-20 09:24:05,079 * INFO * [209487] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.75-1.79
2015-07-20 09:24:06,092 * INFO * [207379] percTaxaIncorpUnif/DESeq2/75/50/1.69-1.75 Finished with 0
2015-07-20 09:24:06,094 * INFO * [209530] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.69-1.75
2015-07-20 09:24:08,265 * INFO * [207391] percTaxaIncorpUnif/DESeq2/75/50/1.67-1.75 Finished with 0
2015-07-20 09:24:08,268 * INFO * [209574] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.67-1.75
2015-07-20 09:24:08,367 * INFO * [207365] percTaxaIncorpUnif/DESeq2/75/50/1.75-1.79 Finished with 0
2015-07-20 09:24:08,369 * INFO * [209593] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.75-1.77
2015-07-20 09:24:08,494 * INFO * [207076] percTaxaIncorpUnif/DESeq2/75/50/1.73-1.79 Finished with 0
2015-07-20 09:24:08,497 * INFO * [209614] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.67-1.81
2015-07-20 09:24:09,224 * INFO * [207245] percTaxaIncorpUnif/DESeq2/75/50/1.69-1.79 Finished with 0
2015-07-20 09:24:09,226 * INFO * [209653] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.73-1.75
2015-07-20 09:24:12,850 * INFO * [207314] percTaxaIncorpUnif/DESeq2/75/50/1.67-1.77 Finished with 0
2015-07-20 09:24:12,853 * INFO * [209730] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.71-1.77
2015-07-20 09:24:16,405 * INFO * [207742] percTaxaIncorpUnif/DESeq2/75/50/1.73-1.75 Finished with 0
2015-07-20 09:24:16,408 * INFO * [209891] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.69-1.81
2015-07-20 09:24:19,342 * INFO * [207482] percTaxaIncorpUnif/DESeq2/75/50/1.75-1.77 Finished with 0
2015-07-20 09:24:19,344 * INFO * [209963] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.67-1.71
2015-07-20 09:24:21,375 * INFO * [207757] percTaxaIncorpUnif/DESeq2/75/50/1.71-1.77 Finished with 0
2015-07-20 09:24:21,377 * INFO * [210007] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.73-1.81
2015-07-20 09:24:21,782 * INFO * [207627] percTaxaIncorpUnif/DESeq2/75/50/1.67-1.81 Finished with 0
2015-07-20 09:24:21,784 * INFO * [210020] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.71-1.81
2015-07-20 09:24:29,686 * INFO * [207874] percTaxaIncorpUnif/DESeq2/75/50/1.69-1.81 Finished with 0
2015-07-20 09:24:29,689 * INFO * [210267] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.71-1.79
2015-07-20 09:24:49,956 * INFO * [208672] percTaxaIncorpUnif/DESeq2/75/50/1.71-1.79 Finished with 0
2015-07-20 09:24:49,959 * INFO * [210780] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.67-1.73
2015-07-20 09:24:53,620 * INFO * [208535] percTaxaIncorpUnif/DESeq2/75/50/1.67-1.71 Finished with 0
2015-07-20 09:24:53,623 * INFO * [210895] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/75/1.77-1.79
2015-07-20 09:24:54,657 * INFO * [208649] percTaxaIncorpUnif/DESeq2/75/50/1.71-1.81 Finished with 0
2015-07-20 09:24:54,660 * INFO * [210942] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.67-1.79
2015-07-20 09:24:55,470 * INFO * [208772] percTaxaIncorpUnif/DESeq2/75/50/1.77-1.79 Finished with 0
2015-07-20 09:24:55,472 * INFO * [210989] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.73-1.77
2015-07-20 09:24:55,992 * INFO * [208636] percTaxaIncorpUnif/DESeq2/75/50/1.73-1.81 Finished with 0
2015-07-20 09:24:55,994 * INFO * [211002] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.69-1.77
2015-07-20 09:24:56,472 * INFO * [208759] percTaxaIncorpUnif/DESeq2/75/50/1.67-1.73 Finished with 0
2015-07-20 09:24:56,474 * INFO * [211029] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.71-1.75
2015-07-20 09:25:05,019 * INFO * [209051] percTaxaIncorpUnif/DESeq2/75/75/1.73-1.77 Finished with 0
2015-07-20 09:25:05,022 * INFO * [211243] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.75-1.81
2015-07-20 09:25:07,871 * INFO * [209119] percTaxaIncorpUnif/DESeq2/75/75/1.71-1.75 Finished with 0
2015-07-20 09:25:07,874 * INFO * [211314] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.71-1.73
2015-07-20 09:25:08,769 * INFO * [209393] percTaxaIncorpUnif/DESeq2/75/75/1.69-1.73 Finished with 0
2015-07-20 09:25:08,771 * INFO * [211349] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.73-1.79
2015-07-20 09:25:10,807 * INFO * [208988] percTaxaIncorpUnif/DESeq2/75/75/1.67-1.79 Finished with 0
2015-07-20 09:25:10,810 * INFO * [211393] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.69-1.71
2015-07-20 09:25:13,419 * INFO * [209202] percTaxaIncorpUnif/DESeq2/75/75/1.75-1.81 Finished with 0
2015-07-20 09:25:13,422 * INFO * [211470] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.77-1.81
2015-07-20 09:25:14,060 * INFO * [209102] percTaxaIncorpUnif/DESeq2/75/75/1.69-1.77 Finished with 0
2015-07-20 09:25:14,062 * INFO * [211495] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.69-1.73
2015-07-20 09:25:14,899 * INFO * [209359] percTaxaIncorpUnif/DESeq2/75/75/1.69-1.71 Finished with 0
2015-07-20 09:25:14,901 * INFO * [211537] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.69-1.79
2015-07-20 09:25:15,427 * INFO * [209653] percTaxaIncorpUnif/DESeq2/75/75/1.73-1.75 Finished with 0
2015-07-20 09:25:15,429 * INFO * [211581] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.67-1.77
2015-07-20 09:25:16,591 * INFO * [209372] percTaxaIncorpUnif/DESeq2/75/75/1.77-1.81 Finished with 0
2015-07-20 09:25:16,593 * INFO * [211622] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.75-1.79
2015-07-20 09:25:17,162 * INFO * [209298] percTaxaIncorpUnif/DESeq2/75/75/1.73-1.79 Finished with 0
2015-07-20 09:25:17,164 * INFO * [211649] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.69-1.75
2015-07-20 09:25:18,214 * INFO * [209263] percTaxaIncorpUnif/DESeq2/75/75/1.71-1.73 Finished with 0
2015-07-20 09:25:18,217 * INFO * [211688] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.67-1.75
2015-07-20 09:25:18,569 * INFO * [209487] percTaxaIncorpUnif/DESeq2/75/75/1.75-1.79 Finished with 0
2015-07-20 09:25:18,572 * INFO * [211701] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.75-1.77
2015-07-20 09:25:19,328 * INFO * [209406] percTaxaIncorpUnif/DESeq2/75/75/1.69-1.79 Finished with 0
2015-07-20 09:25:19,331 * INFO * [211723] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.67-1.81
2015-07-20 09:25:21,014 * INFO * [209614] percTaxaIncorpUnif/DESeq2/75/75/1.67-1.81 Finished with 0
2015-07-20 09:25:21,016 * INFO * [211773] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.73-1.75
2015-07-20 09:25:24,057 * INFO * [209574] percTaxaIncorpUnif/DESeq2/75/75/1.67-1.75 Finished with 0
2015-07-20 09:25:24,059 * INFO * [211834] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.71-1.77
2015-07-20 09:25:25,722 * INFO * [209431] percTaxaIncorpUnif/DESeq2/75/75/1.67-1.77 Finished with 0
2015-07-20 09:25:25,725 * INFO * [211897] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.69-1.81
2015-07-20 09:25:25,835 * INFO * [209593] percTaxaIncorpUnif/DESeq2/75/75/1.75-1.77 Finished with 0
2015-07-20 09:25:25,837 * INFO * [211919] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.67-1.71
2015-07-20 09:25:27,251 * INFO * [209963] percTaxaIncorpUnif/DESeq2/75/75/1.67-1.71 Finished with 0
2015-07-20 09:25:27,254 * INFO * [211983] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.73-1.81
2015-07-20 09:25:29,075 * INFO * [209530] percTaxaIncorpUnif/DESeq2/75/75/1.69-1.75 Finished with 0
2015-07-20 09:25:29,078 * INFO * [212030] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.71-1.81
2015-07-20 09:25:29,380 * INFO * [209730] percTaxaIncorpUnif/DESeq2/75/75/1.71-1.77 Finished with 0
2015-07-20 09:25:29,382 * INFO * [212043] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.71-1.79
2015-07-20 09:25:38,632 * INFO * [210007] percTaxaIncorpUnif/DESeq2/75/75/1.73-1.81 Finished with 0
2015-07-20 09:25:38,635 * INFO * [212312] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.67-1.73
2015-07-20 09:25:39,655 * INFO * [209891] percTaxaIncorpUnif/DESeq2/75/75/1.69-1.81 Finished with 0
2015-07-20 09:25:39,659 * INFO * [212341] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/0/1.77-1.79
2015-07-20 09:25:42,220 * INFO * [210020] percTaxaIncorpUnif/DESeq2/75/75/1.71-1.81 Finished with 0
2015-07-20 09:25:42,222 * INFO * [212430] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/100/1.67-1.79
2015-07-20 09:25:47,519 * INFO * [210267] percTaxaIncorpUnif/DESeq2/75/75/1.71-1.79 Finished with 0
2015-07-20 09:25:47,523 * INFO * [212581] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/100/1.73-1.77
2015-07-20 09:26:03,723 * INFO * [210895] percTaxaIncorpUnif/DESeq2/75/75/1.77-1.79 Finished with 0
2015-07-20 09:26:03,726 * INFO * [212978] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/100/1.69-1.77
2015-07-20 09:26:05,107 * INFO * [211002] percTaxaIncorpUnif/DESeq2/75/0/1.69-1.77 Finished with 0
2015-07-20 09:26:05,113 * INFO * [213017] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/100/1.71-1.75
2015-07-20 09:26:05,431 * INFO * [210942] percTaxaIncorpUnif/DESeq2/75/0/1.67-1.79 Finished with 0
2015-07-20 09:26:05,434 * INFO * [213039] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/100/1.75-1.81
2015-07-20 09:26:13,323 * INFO * [211029] percTaxaIncorpUnif/DESeq2/75/0/1.71-1.75 Finished with 0
2015-07-20 09:26:13,326 * INFO * [213258] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/100/1.71-1.73
2015-07-20 09:26:14,146 * INFO * [210780] percTaxaIncorpUnif/DESeq2/75/75/1.67-1.73 Finished with 0
2015-07-20 09:26:14,148 * INFO * [213283] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/100/1.73-1.79
2015-07-20 09:26:15,190 * INFO * [210989] percTaxaIncorpUnif/DESeq2/75/0/1.73-1.77 Finished with 0
2015-07-20 09:26:15,193 * INFO * [213328] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/100/1.69-1.71
2015-07-20 09:26:24,617 * INFO * [211243] percTaxaIncorpUnif/DESeq2/75/0/1.75-1.81 Finished with 0
2015-07-20 09:26:24,620 * INFO * [213535] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/75/100/1.77-1.81
2015-07-20 09:26:24,630 * INFO * [211470] percTaxaIncorpUnif/DESeq2/75/0/1.77-1.81 Finished with 0
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2015-07-20 09:36:33,209 * INFO * [229199] percTaxaIncorpUnif/DESeq2/25/75/1.77-1.81 Finished with 0
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2015-07-20 09:39:36,972 * INFO * [234832] percTaxaIncorpUnif/DESeq2/25/25/1.77-1.81 Finished with 0
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2015-07-20 09:49:41,491 * INFO * [7204] percTaxaIncorpUnif/DESeq2/5/100/1.69-1.71 Finished with 0
2015-07-20 09:49:41,494 * INFO * [9814] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.67-1.77
2015-07-20 09:49:42,672 * INFO * [7185] percTaxaIncorpUnif/DESeq2/5/100/1.73-1.79 Finished with 0
2015-07-20 09:49:42,675 * INFO * [9884] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.75-1.79
2015-07-20 09:49:44,450 * INFO * [7220] percTaxaIncorpUnif/DESeq2/5/100/1.77-1.81 Finished with 0
2015-07-20 09:49:44,452 * INFO * [9928] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.69-1.75
2015-07-20 09:49:48,159 * INFO * [7400] percTaxaIncorpUnif/DESeq2/5/100/1.69-1.79 Finished with 0
2015-07-20 09:49:48,162 * INFO * [10043] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.67-1.75
2015-07-20 09:49:48,297 * INFO * [7465] percTaxaIncorpUnif/DESeq2/5/100/1.75-1.79 Finished with 0
2015-07-20 09:49:48,300 * INFO * [10058] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.75-1.77
2015-07-20 09:49:49,200 * INFO * [7441] percTaxaIncorpUnif/DESeq2/5/100/1.67-1.77 Finished with 0
2015-07-20 09:49:49,202 * INFO * [10089] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.67-1.81
2015-07-20 09:49:56,061 * INFO * [7488] percTaxaIncorpUnif/DESeq2/5/100/1.69-1.75 Finished with 0
2015-07-20 09:49:56,064 * INFO * [10254] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.73-1.75
2015-07-20 09:49:57,925 * INFO * [7742] percTaxaIncorpUnif/DESeq2/5/100/1.75-1.77 Finished with 0
2015-07-20 09:49:57,928 * INFO * [10317] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.71-1.77
2015-07-20 09:49:59,510 * INFO * [7761] percTaxaIncorpUnif/DESeq2/5/100/1.67-1.81 Finished with 0
2015-07-20 09:49:59,512 * INFO * [10387] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.69-1.81
2015-07-20 09:49:59,633 * INFO * [7784] percTaxaIncorpUnif/DESeq2/5/100/1.73-1.75 Finished with 0
2015-07-20 09:49:59,635 * INFO * [10403] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.67-1.71
2015-07-20 09:49:59,699 * INFO * [7729] percTaxaIncorpUnif/DESeq2/5/100/1.67-1.75 Finished with 0
2015-07-20 09:49:59,701 * INFO * [10416] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.73-1.81
2015-07-20 09:50:01,590 * INFO * [7982] percTaxaIncorpUnif/DESeq2/5/100/1.71-1.77 Finished with 0
2015-07-20 09:50:01,593 * INFO * [10453] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.71-1.81
2015-07-20 09:50:10,728 * INFO * [8503] percTaxaIncorpUnif/DESeq2/5/100/1.69-1.81 Finished with 0
2015-07-20 09:50:10,731 * INFO * [10758] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.71-1.79
2015-07-20 09:50:11,577 * INFO * [8550] percTaxaIncorpUnif/DESeq2/5/100/1.67-1.71 Finished with 0
2015-07-20 09:50:11,581 * INFO * [10787] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.67-1.73
2015-07-20 09:50:16,647 * INFO * [8618] percTaxaIncorpUnif/DESeq2/5/100/1.71-1.81 Finished with 0
2015-07-20 09:50:16,649 * INFO * [10896] Started ./SIPSimRun.sh in percTaxaIncorpUnif/DESeq2/5/25/1.77-1.79
2015-07-20 09:50:19,412 * INFO * [8563] percTaxaIncorpUnif/DESeq2/5/100/1.73-1.81 Finished with 0
2015-07-20 09:50:21,727 * INFO * [8889] percTaxaIncorpUnif/DESeq2/5/100/1.71-1.79 Finished with 0
2015-07-20 09:50:27,756 * INFO * [9102] percTaxaIncorpUnif/DESeq2/5/100/1.77-1.79 Finished with 0
2015-07-20 09:50:36,182 * INFO * [9139] percTaxaIncorpUnif/DESeq2/5/25/1.67-1.79 Finished with 0
2015-07-20 09:50:36,636 * INFO * [9419] percTaxaIncorpUnif/DESeq2/5/25/1.75-1.81 Finished with 0
2015-07-20 09:50:36,841 * INFO * [9026] percTaxaIncorpUnif/DESeq2/5/100/1.67-1.73 Finished with 0
2015-07-20 09:50:37,045 * INFO * [9474] percTaxaIncorpUnif/DESeq2/5/25/1.69-1.71 Finished with 0
2015-07-20 09:50:38,283 * INFO * [9232] percTaxaIncorpUnif/DESeq2/5/25/1.73-1.77 Finished with 0
2015-07-20 09:50:38,325 * INFO * [9448] percTaxaIncorpUnif/DESeq2/5/25/1.71-1.73 Finished with 0
2015-07-20 09:50:39,316 * INFO * [9343] percTaxaIncorpUnif/DESeq2/5/25/1.69-1.77 Finished with 0
2015-07-20 09:50:40,782 * INFO * [9461] percTaxaIncorpUnif/DESeq2/5/25/1.73-1.79 Finished with 0
2015-07-20 09:50:41,597 * INFO * [9406] percTaxaIncorpUnif/DESeq2/5/25/1.71-1.75 Finished with 0
2015-07-20 09:50:45,538 * INFO * [9676] percTaxaIncorpUnif/DESeq2/5/25/1.69-1.73 Finished with 0
2015-07-20 09:50:45,868 * INFO * [9609] percTaxaIncorpUnif/DESeq2/5/25/1.77-1.81 Finished with 0
2015-07-20 09:50:52,243 * INFO * [9928] percTaxaIncorpUnif/DESeq2/5/25/1.69-1.75 Finished with 0
2015-07-20 09:50:53,647 * INFO * [10058] percTaxaIncorpUnif/DESeq2/5/25/1.75-1.77 Finished with 0
2015-07-20 09:50:54,378 * INFO * [9884] percTaxaIncorpUnif/DESeq2/5/25/1.75-1.79 Finished with 0
2015-07-20 09:50:57,516 * INFO * [10043] percTaxaIncorpUnif/DESeq2/5/25/1.67-1.75 Finished with 0
2015-07-20 09:50:57,766 * INFO * [9814] percTaxaIncorpUnif/DESeq2/5/25/1.67-1.77 Finished with 0
2015-07-20 09:50:57,927 * INFO * [9763] percTaxaIncorpUnif/DESeq2/5/25/1.69-1.79 Finished with 0
2015-07-20 09:51:00,621 * INFO * [10089] percTaxaIncorpUnif/DESeq2/5/25/1.67-1.81 Finished with 0
2015-07-20 09:51:02,808 * INFO * [10453] percTaxaIncorpUnif/DESeq2/5/25/1.71-1.81 Finished with 0
2015-07-20 09:51:03,435 * INFO * [10317] percTaxaIncorpUnif/DESeq2/5/25/1.71-1.77 Finished with 0
2015-07-20 09:51:03,997 * INFO * [10416] percTaxaIncorpUnif/DESeq2/5/25/1.73-1.81 Finished with 0
2015-07-20 09:51:04,218 * INFO * [10254] percTaxaIncorpUnif/DESeq2/5/25/1.73-1.75 Finished with 0
2015-07-20 09:51:06,454 * INFO * [10387] percTaxaIncorpUnif/DESeq2/5/25/1.69-1.81 Finished with 0
2015-07-20 09:51:08,225 * INFO * [10403] percTaxaIncorpUnif/DESeq2/5/25/1.67-1.71 Finished with 0
2015-07-20 09:51:08,638 * INFO * [10787] percTaxaIncorpUnif/DESeq2/5/25/1.67-1.73 Finished with 0
2015-07-20 09:51:12,583 * INFO * [10896] percTaxaIncorpUnif/DESeq2/5/25/1.77-1.79 Finished with 0
2015-07-20 09:51:14,193 * INFO * [10758] percTaxaIncorpUnif/DESeq2/5/25/1.71-1.79 Finished with 0



In [121]:

    
# Creating NA tables for any failures
sDir = os.path.join(buildDir, 'DESeq2', '*', '*', '*')
dirs = glob.glob(sDir)

tbl = """
,byClass
Sensitivity,NA
Specificity,NA
Pos Pred Value,NA
Neg Pred Value,NA
Prevalence,NA
Detection Rate,NA
Detection Prevalence,NA
Balanced Accuracy,NA
"""

for x in dirs:
    f = os.path.join(x, 'DESeq2-cMtx_byClass.csv')
    if not os.path.isfile(f):
        with open(f, 'wb') as inFH:
            inFH.write(tbl)



In [123]:

    
# aggregating confusion matrix data
## table
# !cd $buildDir; \
#     nestagg delim \
#         -d DESeq2 \
#         -k percIncorp,percTaxaIncorp,BD_min,BD_max \
#         -o ./DESeq2/cMtx_table.csv \
#         DESeq2-cMtx_table.csv

# ## overall
# !cd $buildDir; \
#     nestagg delim \
#         -d DESeq2 \
#         -k percIncorp,percTaxaIncorp,BD_min,BD_max \
#         -o ./DESeq2/cMtx_overall.csv \
#         DESeq2-cMtx_overall.csv
    
## byClass
!cd $buildDir; \
    nestagg delim \
        -d DESeq2 \
        -k percIncorp,percTaxaIncorp,BD_min,BD_max \
        -o ./DESeq2/cMtx_byClass.csv \
        DESeq2-cMtx_byClass.csv

Plotting results



In [124]:

    
%%R -i buildDir -w 600 -h 600
setwd(buildDir)

byClass = read.csv('./DESeq2/cMtx_byClass.csv')

byClass$byClass[is.na(byClass$byClass)] = 0

byClass %>% head









    





               X   byClass percTaxaIncorp percIncorp BD_min BD_max
1    Sensitivity 0.0000000             50         50   1.67   1.79
2    Specificity 1.0000000             50         50   1.67   1.79
3 Pos Pred Value 0.0000000             50         50   1.67   1.79
4 Neg Pred Value 0.4868996             50         50   1.67   1.79
5     Prevalence 0.5131004             50         50   1.67   1.79
6 Detection Rate 0.0000000             50         50   1.67   1.79



In [126]:

    
%%R -w 800 -h 750

col2keep = c('Balanced Accuracy', 'Sensitivity','Specificity')
byClass.f = byClass %>%
    filter(X %in% col2keep) %>%
    mutate(BD_min = as.numeric(BD_min),
           BD_max = as.numeric(BD_max),
           byClass = as.numeric(byClass),
           byClass.inv = 1 - byClass) 

byClass.fs = byClass.f %>%
    group_by(X, percIncorp, percTaxaIncorp) %>%
    summarize(byClass.max = max(byClass))

just.true = function(x){
    if(x == TRUE){
        return(1)
        } else{
        return(NA)
        }
    }

byClass.j = inner_join(byClass.f, byClass.fs, c('X' = 'X',
                                                'percIncorp' = 'percIncorp',
                                                'percTaxaIncorp' = 'percTaxaIncorp')) %>%
    mutate(max_val = as.numeric(byClass == byClass.max),
           byClass.txt = round(byClass, 2))
byClass.jf = byClass.j %>%
    filter(max_val == 1)

byClass.j %>% head









    





                  X    byClass percTaxaIncorp percIncorp BD_min BD_max
1       Sensitivity 0.00000000             50         50   1.67   1.79
2       Specificity 1.00000000             50         50   1.67   1.79
3 Balanced Accuracy 0.50000000             50         50   1.67   1.79
4       Sensitivity 0.08121827             50         50   1.73   1.77
5       Specificity 1.00000000             50         50   1.73   1.77
6 Balanced Accuracy 0.54060914             50         50   1.73   1.77
  byClass.inv byClass.max max_val byClass.txt
1   1.0000000   0.9444444       0        0.00
2   0.0000000   1.0000000       1        1.00
3   0.5000000   0.7500000       0        0.50
4   0.9187817   0.9444444       0        0.08
5   0.0000000   1.0000000       1        1.00
6   0.4593909   0.7500000       0        0.54



In [ ]:

    
%%R

x.breaks = unique(byClass.j$BD_min)

taxaIncorp = unique(byClass.j$percTaxaIncorp)

for (x in taxaIncorp){
    tbl = byClass.j %>% filter(percTaxaIncorp == x)
    
    p = ggplot(tbl, aes(BD_min, BD_max, fill=byClass.inv)) +
    geom_tile() +
    geom_text(aes(label=byClass.txt), color=c('white'), size=4) +
    geom_text(data=byClass.jf, aes(label=byClass.txt), color=c('red'), size=4) +
    scale_x_continuous(breaks=x.breaks) +
    labs(x='Minimum Buoyant Density', y='Maximum Buoyant Density') +
    facet_grid(percIncorp ~ X) +
    theme_bw() +
    theme(
        text=element_text(size=16),
        axis.text.x=element_text(angle=90, hjust=1, vjust=0.5)
        )
    
    print(p)
    }



In [ ]:



In [127]:

    
%%R -i workDir -w 600 -h 600
setwd(workDir)

byClass = read.csv('./percIncorpUnif/DESeq2-cMtx_byClass.csv')

byClass$byClass[is.na(byClass$byClass)] = 0

byClass$percIncorp = factor(byClass$percIncorp, levels=as.character(unique(sort(byClass$percIncorp))))
p = ggplot(byClass, aes(X, byClass, color=percIncorp)) +
    geom_point() +
    labs(y='value') +
    theme_bw() +
    theme(
        text=element_text(size=16),
        axis.text.x=element_text(angle=90, hjust=1, vjust=0.5),
        axis.title.x=element_blank()
        )
p



In [130]:

    
%%R -w 600 -h 400

p + scale_y_continuous(limits=c(0,0.15))

Plotting false negative taxa (actual incorporators)



In [243]:

    
%%R -i workDir

setwd(workDir)

tbl.c = read.csv('percIncorpUnif/50/DESeq2-cMtx_data.csv')

tbl.c.f = tbl.c %>% 
    filter(incorp.known==TRUE & incorp.pred==FALSE) %>%
    select(taxon)

write.table(tbl.c.f, file='percIncorpUnif/50/DESeq2-cMtx_FN', row.names=F, col.names=F, quote=F)



In [250]:

    
!cd $workDir'percIncorpUnif/50/'; \
    $R_dir/OTU_taxonAbund.r OTU_n2_abs1e8_sub30000.txt -t DESeq2-cMtx_FN -l -o DESeq2-cMtx_FN --width 14









    



File written: DESeq2-cMtx_FN_abs-abund.pdf
Warning messages:
1: Removed 48 rows containing missing values (position_stack). 
2: Removed 16 rows containing missing values (position_stack). 
File written: DESeq2-cMtx_FN_rel-abund.pdf



In [252]:

    
%%R -i workDir

setwd(workDir)

tbl.c = read.csv('percIncorpUnif/50/DESeq2-cMtx_data.csv')

tbl.c.f = tbl.c %>% 
    filter(incorp.known==FALSE & incorp.pred==TRUE) %>%
    select(taxon)

write.table(tbl.c.f, file='percIncorpUnif/50/DESeq2-cMtx_FP', row.names=F, col.names=F, quote=F)



In [253]:

    
!cd $workDir'percIncorpUnif/50/'; \
    $R_dir/OTU_taxonAbund.r OTU_n2_abs1e8_sub30000.txt -t DESeq2-cMtx_FP -l -o DESeq2-cMtx_FP --width 14









    



File written: DESeq2-cMtx_FP_abs-abund.pdf
Warning messages:
1: Removed 9 rows containing missing values (position_stack). 
2: Removed 3 rows containing missing values (position_stack). 
File written: DESeq2-cMtx_FP_rel-abund.pdf



In [256]:

    
%%R
tbl.c %>% filter(taxon %in% tbl.c.f$taxon)









    





  lib1 lib2                                    taxon BD_shift incorp.known
1   NA    2 Corynebacterium_pseudotuberculosis_FRC41        0        FALSE
2   NA    2            Anaplasma_centrale_str_Israel        0        FALSE
3   NA    2         Dyadobacter_fermentans_DSM_18053        0        FALSE
   baseMean log2FoldChange     lfcSE     stat       pvalue        padj
1 2.3478747       3.801071 0.8494856 4.474555 7.657045e-06 0.000344567
2 0.9337178       4.130228 1.0213776 4.043782 5.259585e-05 0.001183407
3 1.0835454       3.158858 0.8578349 3.682362 2.310831e-04 0.003466247
  incorp.pred
1        TRUE
2        TRUE
3        TRUE

Enrichment of TP for abundant incorporators?

What is the abundance distribution of TP and FP?
- Are more abundant incorporators being detected more than low abundant taxa



In [200]:

    
%%R -i workDir

setwd(workDir)

tbl.c = read.csv('percIncorpUnif/100/DESeq2-cMtx_data.csv')
tbl.otu = read.delim('percIncorpUnif/100/OTU_n2_abs1e10_sub20000.txt', sep='\t')



In [201]:

    
%%R
# OTU total counts
tbl.otu.sum = tbl.otu %>%
    group_by(library, taxon) %>%
    summarize(total_count = sum(count))
tbl.otu.sum %>% head









    





Source: local data frame [6 x 3]
Groups: library

  library                                taxon total_count
1       1       Acaryochloris_marina_MBIC11017           0
2       1       Acetobacterium_woodii_DSM_1030           0
3       1 Acetobacter_pasteurianus_IFO_3283-12         751
4       1    Acetohalobium_arabaticum_DSM_5501           9
5       1         Acholeplasma_laidlawii_PG-8A         238
6       1        Achromobacter_xylosoxidans_A8          17



In [202]:

    
%%R
# 
label.tp.fn = function(known, pred){
    if(is.na(known) | is.na(pred)){
        return(NA)
        } else
    if(known==TRUE & pred==TRUE){
        return('TP')
        } else
    if(known==TRUE & pred==FALSE){
        return('FN')
        } else {
        return(NA)
        }
    }

tbl.c.tp.fn = tbl.c %>% 
    mutate(tp.fn = mapply(label.tp.fn, incorp.known, incorp.pred)) %>%
    filter(! is.na(tp.fn))

tbl.tp.fn = inner_join(tbl.c.tp.fn, tbl.otu.sum, c('taxon' = 'taxon')) 
tbl.tp.fn %>% head









    





  lib1 lib2                              taxon  BD_shift incorp.known  baseMean
1   NA    2 Actinobacillus_equuli_subsp_equuli 0.9999269         TRUE 1.8646755
2   NA    2 Actinobacillus_equuli_subsp_equuli 0.9999269         TRUE 1.8646755
3   NA    2 Candidatus_Moranella_endobia_PCVAL 0.9997449         TRUE 0.4688403
4   NA    2 Candidatus_Moranella_endobia_PCVAL 0.9997449         TRUE 0.4688403
5   NA    2     Alkaliphilus_oremlandii_OhILAs 0.9997434         TRUE 0.3118965
6   NA    2     Alkaliphilus_oremlandii_OhILAs 0.9997434         TRUE 0.3118965
  log2FoldChange    lfcSE       stat       pvalue       padj            p
1     5.37154211 1.267839 4.23676891 2.267593e-05 0.00111679 2.677315e-05
2     5.37154211 1.267839 4.23676891 2.267593e-05 0.00111679 2.677315e-05
3     0.04533956 1.501490 0.03019637 9.759104e-01 1.00000000 5.542099e-01
4     0.04533956 1.501490 0.03019637 9.759104e-01 1.00000000 5.542099e-01
5     5.33532814 1.665671 3.20311065 1.359517e-03 0.02434772 1.132750e-03
6     5.33532814 1.665671 3.20311065 1.359517e-03 0.02434772 1.132750e-03
      padj.BH incorp.pred tp.fn library total_count
1 0.001318578        TRUE    TP       1        1728
2 0.001318578        TRUE    TP       2        1554
3 1.000000000       FALSE    FN       1         371
4 1.000000000       FALSE    FN       2        1981
5 0.022315185        TRUE    TP       1         183
6 0.022315185        TRUE    TP       2         247



In [203]:

    
%%R
# how many TP & FN?
tbl.tp.fn %>% 
    group_by(library, tp.fn) %>%
    summarize(n = n())









    





Source: local data frame [4 x 3]
Groups: library

  library tp.fn  n
1       1    FN 63
2       1    TP  9
3       2    FN 63
4       2    TP  9



In [204]:

    
%%R -h 350
tbl.tp.fn$library = as.character(tbl.tp.fn$library)
ggplot(tbl.tp.fn, aes(library, total_count, color=tp.fn)) +
    geom_boxplot() +
    labs(y='Total count') +
    theme(
        text = element_text(size=18)
        )



In [209]:

    
%%R -h 700 -w 900
tbl.tp.fn$library = as.character(tbl.tp.fn$library)
ggplot(tbl.tp.fn, aes(taxon, total_count, group=taxon, color=library)) +
    geom_point(size=3) +
    geom_line() +
    scale_y_log10() +
    labs(y='Total count') +
    facet_grid(. ~ tp.fn, scales='free_x') +
    theme(
        text = element_text(size=18),
        axis.text.x = element_text(angle=90, hjust=1)
        )

Notes:

FNs can be abundant
TP can have a lower abundance in the 'treatment' library

Just looking at the 'heavy' fractions



In [210]:

    
%%R
# OTU total counts

heavy.cut = 1.71

tbl.otu.sum = tbl.otu %>%
    filter(! grepl('inf', fraction)) %>%
    separate(fraction, into = c('BD_min','BD_max'), sep='-', convert=TRUE) %>%
    filter(BD_min >= heavy.cut & BD_max <= 2) %>%
    group_by(library, taxon) %>%
    summarize(total_count = sum(count))
tbl.otu.sum %>% head









    





Source: local data frame [6 x 3]
Groups: library

  library                                taxon total_count
1       1       Acaryochloris_marina_MBIC11017           0
2       1       Acetobacterium_woodii_DSM_1030           0
3       1 Acetobacter_pasteurianus_IFO_3283-12         564
4       1    Acetohalobium_arabaticum_DSM_5501           0
5       1         Acholeplasma_laidlawii_PG-8A           0
6       1        Achromobacter_xylosoxidans_A8          17



In [211]:

    
%%R

tbl.tp.fn = inner_join(tbl.c.tp.fn, tbl.otu.sum, c('taxon' = 'taxon')) 
tbl.tp.fn %>% head









    





  lib1 lib2                              taxon  BD_shift incorp.known  baseMean
1   NA    2 Actinobacillus_equuli_subsp_equuli 0.9999269         TRUE 1.8646755
2   NA    2 Actinobacillus_equuli_subsp_equuli 0.9999269         TRUE 1.8646755
3   NA    2 Candidatus_Moranella_endobia_PCVAL 0.9997449         TRUE 0.4688403
4   NA    2 Candidatus_Moranella_endobia_PCVAL 0.9997449         TRUE 0.4688403
5   NA    2     Alkaliphilus_oremlandii_OhILAs 0.9997434         TRUE 0.3118965
6   NA    2     Alkaliphilus_oremlandii_OhILAs 0.9997434         TRUE 0.3118965
  log2FoldChange    lfcSE       stat       pvalue       padj            p
1     5.37154211 1.267839 4.23676891 2.267593e-05 0.00111679 2.677315e-05
2     5.37154211 1.267839 4.23676891 2.267593e-05 0.00111679 2.677315e-05
3     0.04533956 1.501490 0.03019637 9.759104e-01 1.00000000 5.542099e-01
4     0.04533956 1.501490 0.03019637 9.759104e-01 1.00000000 5.542099e-01
5     5.33532814 1.665671 3.20311065 1.359517e-03 0.02434772 1.132750e-03
6     5.33532814 1.665671 3.20311065 1.359517e-03 0.02434772 1.132750e-03
      padj.BH incorp.pred tp.fn library total_count
1 0.001318578        TRUE    TP       1        1383
2 0.001318578        TRUE    TP       2        1554
3 1.000000000       FALSE    FN       1          30
4 1.000000000       FALSE    FN       2        1981
5 0.022315185        TRUE    TP       1           0
6 0.022315185        TRUE    TP       2         246



In [212]:

    
%%R -h 350
tbl.tp.fn$library = as.character(tbl.tp.fn$library)
ggplot(tbl.tp.fn, aes(library, total_count, color=tp.fn)) +
    geom_boxplot() +
    labs(y='Total count') +
    theme(
        text = element_text(size=18)
        )



In [215]:

    
%%R -h 700 -w 900
tbl.tp.fn$library = as.character(tbl.tp.fn$library)
ggplot(tbl.tp.fn, aes(taxon, total_count, group=taxon, color=library)) +
    geom_point(size=3) +
    geom_line() +
    scale_y_log10() +
    labs(y='Total count') +
    facet_grid(. ~ tp.fn, scales='free_x') +
    theme(
        text = element_text(size=18),
        axis.text.x = element_text(angle=90, hjust=1)
        )



In [ ]:

    
%%R -i workDir -w 1000 -h 450
setwd(workDir)

tbl.ds = read.csv('DESeq2-cMtx_data.csv')

# loading file
tbl.otu = read.delim('OTU_abs1e10.txt', sep='\t')

tbl.otu = tbl.otu %>% 
    filter(!grepl('inf', fraction, ignore.case=T)) %>%
    separate(fraction, into = c('BD_min','BD_max'), sep='-', convert=TRUE) %>%

tbl.j = inner_join(tbl.otu, tbl.ds, c('taxon' = 'taxon'))

Notes:

The TPs (for the most part) are dramatically different in abundance between control and treatment

Sandbox



In [ ]:



In [73]:

    
# building tree structure
from os.path import abspath
nest = nestly.Nest()

##  values
vals = [str(x) for x in range(1,5)]
nest.add('vals', vals)


## input files
nest.add('--np', [1], create_dir=False)

buildDir = '/home/nick/t/nestly/' #os.path.join(workDir, 'vals')
nest.build(buildDir)



In [74]:

    
%%writefile /home/nick/t/example.sh
#!/bin/bash

export TIME='elapsed,maxmem,exitstatus\n%e,%M,%x'

echo {--np} > {--np}_test.txt









    



Writing /home/nick/t/example.sh



In [75]:

    
!cd /home/nick/t/; \
    chmod 777 example.sh



In [76]:

    
!cd /home/nick/t/; \
    nestrun -j 2 --template-file example.sh -d nestly









    



2015-06-24 12:13:25,688 * INFO * Template: ./example.sh
2015-06-24 12:13:25,690 * INFO * [204263] Started ./example.sh in nestly/3
2015-06-24 12:13:25,692 * INFO * [204264] Started ./example.sh in nestly/2
2015-06-24 12:13:25,692 * INFO * [204263] nestly/3 Finished with 0
2015-06-24 12:13:25,694 * INFO * [204265] Started ./example.sh in nestly/1
2015-06-24 12:13:25,694 * INFO * [204264] nestly/2 Finished with 0
2015-06-24 12:13:25,696 * INFO * [204266] Started ./example.sh in nestly/4
2015-06-24 12:13:25,696 * INFO * [204265] nestly/1 Finished with 0
2015-06-24 12:13:25,696 * INFO * [204266] nestly/4 Finished with 0



In [ ]:



In [ ]:



In [120]:

    
%%writefile $bashFile
#!/bin/bash


#-- R analysis --#
export PATH={R_dir}:$PATH
# plotting taxon abundances
OTU_taxonAbund.r \
    OTU_n2_abs{abs}_sub{subsample}.txt \
    -r {topTaxaToPlot} \
    -o OTU_n2_abs{abs}_sub{subsample} 
# running DeSeq2 and making confusion matrix on predicting incorporators
## making phyloseq object from OTU table
phyloseq_make.r \
    OTU_n2_abs{abs}_sub{subsample}_w.txt \
    -s OTU_n2_abs{abs}_sub{subsample}_meta.txt \
    > OTU_n2_abs{abs}_sub{subsample}.physeq
## filtering phyloseq object to just taxa/samples of interest
phyloseq_edit.r \
    OTU_n2_abs{abs}_sub{subsample}.physeq \
    --BD_min {BD_min} --BD_max {BD_max} \
    > OTU_n2_abs{abs}_sub{subsample}_filt.physeq
## making ordination
phyloseq_ordination.r \
    OTU_n2_abs{abs}_sub{subsample}_filt.physeq \
    OTU_n2_abs{abs}_sub{subsample}_bray-NMDS.pdf
## DESeq2
phyloseq_DESeq2.r \
    OTU_n2_abs{abs}_sub{subsample}_filt.physeq \
    > OTU_n2_abs{abs}_sub{subsample}_DESeq2
## Confusion matrix
DESeq2_confuseMtx.r \
    {fileName}_kde_dif_incorp_BD-shift.txt \
    OTU_n2_abs{abs}_sub{subsample}_DESeq2 \
    --padj {padj} --log2 {log2}









    



Overwriting /home/nick/notebook/SIPSim/dev/bac_genome1210/SIPSimRun.sh