Running SIPSim pipeline to simulate priming_exp gradient dataset

  • Basing simulation params off of priming_exp dataset
    • Basing starting community diversity on mean percent abundances in all fraction samples for the gradient
    • Other parameters are 'default'

Setting variables


In [15]:
workDir = '/home/nick/notebook/SIPSim/dev/priming_exp/validation_sample/X12C.700.14_fracRichness/'
genomeDir = '/home/nick/notebook/SIPSim/dev/priming_exp/genomes/'
allAmpFrags = '/home/nick/notebook/SIPSim/dev/bac_genome1210/validation/ampFrags.pkl'
otuTableFile = '/var/seq_data/priming_exp/data/otu_table.txt'
metaDataFile = '/var/seq_data/priming_exp/data/allsample_metadata_nomock.txt'
primerFile = '/home/nick/notebook/SIPSim/dev/515F-806R.fna'

cdhit_dir = '/home/nick/notebook/SIPSim/dev/priming_exp/CD-HIT/'
R_dir = '/home/nick/notebook/SIPSim/lib/R/'
figureDir = '/home/nick/notebook/SIPSim/figures/'

# simulation params
comm_richness =  6606
seq_per_fraction = ['lognormal', 10.096, 1.116]

# for making genome_map file for genome fragment simulation
taxonMapFile = os.path.join(cdhit_dir, 'target_taxa.txt')
genomeFilterFile = os.path.join(cdhit_dir, 'genomeFile_seqID_filt.txt')
abundFile = os.path.join('/home/nick/notebook/SIPSim/dev/priming_exp/exp_info', 'X12C.700.14_frac_OTU.txt')

# misc
nprocs = 20

Init


In [2]:
import glob
import cPickle as pickle
import copy
from IPython.display import Image

In [3]:
%load_ext rpy2.ipython

In [4]:
%%R
library(ggplot2)
library(dplyr)
library(tidyr)
library(gridExtra)


/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: 
Attaching package: ‘dplyr’


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: The following objects are masked from ‘package:stats’:

    filter, lag


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: Loading required package: grid

  res = super(Function, self).__call__(*new_args, **new_kwargs)

In [5]:
if not os.path.isdir(workDir):
    os.makedirs(workDir)

Creating a community file from the fraction relative abundances


In [72]:
%%R -i abundFile
# reading priming experiment OTU table
tbl.abund = read.delim(abundFile, sep='\t')
tbl.abund %>% head


      OTUId mean_perc_abund median_perc_abund max_perc_abund      sample
1     OTU.1     3.827532325       3.926317300    5.603168720 X12C.700.14
2    OTU.10     0.048631000       0.048182090    0.085456173 X12C.700.14
3   OTU.100     0.308850910       0.312166472    0.508460092 X12C.700.14
4  OTU.1000     0.013548909       0.013883827    0.024440914 X12C.700.14
5 OTU.10000     0.001464408       0.001464408    0.001464408 X12C.700.14
6  OTU.1001     0.005668025       0.005251645    0.016415420 X12C.700.14

In [73]:
%%R
tbl.comm = tbl.abund %>%
    rename('taxon_name' = OTUId,
           'rel_abund_perc' = mean_perc_abund) %>%
    select(taxon_name, rel_abund_perc) %>%
    mutate(library = '1',
           rank = row_number(-rel_abund_perc)) %>%
    arrange(rank)
    
tbl.comm %>% head


  taxon_name rel_abund_perc library rank
1      OTU.1       3.827532       1    1
2     OTU.68       2.088559       1    2
3      OTU.8       1.422617       1    3
4      OTU.3       1.315828       1    4
5      OTU.7       1.276686       1    5
6      OTU.2       1.264926       1    6

In [74]:
%%R
# rescaling rel_abund_perc so sum(rel_abund_perc) = 100
tbl.comm = tbl.comm %>%
    group_by(library) %>%
    mutate(total = sum(rel_abund_perc)) %>% 
    ungroup() %>%
    mutate(rel_abund_perc = rel_abund_perc * 100 / total) %>%
    select(library, taxon_name, rel_abund_perc, rank)
    
tbl.comm %>% head


Source: local data frame [6 x 4]

  library taxon_name rel_abund_perc rank
1       1      OTU.1       3.194891    1
2       1     OTU.68       1.743347    2
3       1      OTU.8       1.187477    3
4       1      OTU.3       1.098338    4
5       1      OTU.7       1.065667    5
6       1      OTU.2       1.055850    6

In [75]:
%%R -i comm_richness
# number of OTUs
n.OTUs = tbl.comm$taxon_name %>% unique %>% length
cat('Number of OTUs:', n.OTUs, '\n')

# assertion
cat('Community richness = number of OTUs?  ', comm_richness == n.OTUs, '\n')


Number of OTUs: 6606 
Community richness = number of OTUs?   TRUE 

In [76]:
%%R -i workDir

commFile = paste(c(workDir, 'comm.txt'), collapse='/')
write.table(tbl.comm, commFile, sep='\t', quote=F, row.names=F)

Plotting community distribution


In [77]:
%%R -i workDir

commFile = paste(c(workDir, 'comm.txt'), collapse='/')
comm = read.delim(commFile, sep='\t')
comm %>% head


  library taxon_name rel_abund_perc rank
1       1      OTU.1       3.194891    1
2       1     OTU.68       1.743347    2
3       1      OTU.8       1.187477    3
4       1      OTU.3       1.098338    4
5       1      OTU.7       1.065667    5
6       1      OTU.2       1.055850    6

In [78]:
%%R -w 900 -h 350

ggplot(comm, aes(rank, rel_abund_perc)) +
    geom_point() +
    labs(x='Rank', y='% relative abundance', title='Priming experiment community abundance distribution') +
    theme_bw() +
    theme(
        text = element_text(size=16)
        )


Simulating fragments

Making a genome index file to map genome fasta files to OTUs

  • Will be used for community simulation
  • Just OTUs with association to genomes

In [79]:
%%R -i taxonMapFile -i genomeFilterFile 

taxonMap = read.delim(taxonMapFile, sep='\t') %>%
    select(target_genome, OTU) %>%
    distinct()
taxonMap %>% nrow %>% print
taxonMap %>% head(n=3) %>% print

breaker = '----------------\n'
cat(breaker)

genomeFilter = read.delim(genomeFilterFile, sep='\t', header=F) 
genomeFilter %>% nrow %>% print
genomeFilter %>% head(n=3) %>% print

cat(breaker)

comm = read.delim(commFile, sep='\t') 
comm %>% nrow %>% print
comm %>% head(n=3) %>% print


[1] 236
                               target_genome      OTU
1 CP001738_Thermomonospora_curvata_DSM_43183 OTU.8540
2 CP001738_Thermomonospora_curvata_DSM_43183 OTU.9267
3 CP001738_Thermomonospora_curvata_DSM_43183 OTU.1457
----------------
[1] 187
                                                         V1
1                  CP003093_Pseudoxanthomonas_spadix_BD_a59
2                  CP000511_Mycobacterium_vanbaalenii_PYR_1
3 CP003344_Desulfitobacterium_dichloroeliminans_LMG_P_21439
                                                                                                            V2
1                  /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Pseudoxanthomonas_spadix_BD-a59.fasta
2                  /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Mycobacterium_vanbaalenii_PYR-1.fasta
3 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Desulfitobacterium_dichloroeliminans_LMG_P-21439.fasta
----------------
[1] 6606
  library taxon_name rel_abund_perc rank
1       1      OTU.1       3.194891    1
2       1     OTU.68       1.743347    2
3       1      OTU.8       1.187477    3

In [80]:
%%R
taxonMap$OTU %>% table %>% sort(decreasing=T) %>% head


.
    OTU.1    OTU.10   OTU.101   OTU.102 OTU.10237  OTU.1035 
        1         1         1         1         1         1 

In [81]:
%%R

tbl.j = inner_join(taxonMap, genomeFilter, c('target_genome' = 'V1')) %>%
     rename('fasta_file' = V2) %>%
     select(OTU, fasta_file, target_genome)

tbl.j %>% head(n=3)


       OTU
1 OTU.8540
2 OTU.9267
3 OTU.1457
                                                                                     fasta_file
1 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
2 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
3 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
                               target_genome
1 CP001738_Thermomonospora_curvata_DSM_43183
2 CP001738_Thermomonospora_curvata_DSM_43183
3 CP001738_Thermomonospora_curvata_DSM_43183

In [82]:
%%R
tbl.j$OTU %>% table %>% sort(decreasing=T) %>% head


.
    OTU.1    OTU.10   OTU.101   OTU.102 OTU.10237  OTU.1035 
        1         1         1         1         1         1 

In [83]:
%%R
tbl.j2 = inner_join(tbl.j, comm, c('OTU' = 'taxon_name')) 

n.target.genomes = tbl.j2$OTU %>% unique %>% length
cat('Number of target OTUs: ', n.target.genomes, '\n')
cat('--------', '\n')
tbl.j2 %>% head(n=3)


Number of target OTUs:  198 
-------- 
       OTU
1 OTU.8540
2 OTU.9267
3 OTU.1457
                                                                                     fasta_file
1 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
2 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
3 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
                               target_genome library rel_abund_perc rank
1 CP001738_Thermomonospora_curvata_DSM_43183       1    0.002582583 4561
2 CP001738_Thermomonospora_curvata_DSM_43183       1    0.005045402 2191
3 CP001738_Thermomonospora_curvata_DSM_43183       1    0.011258918 1106

In [84]:
%%R -i workDir

outFile = paste(c(workDir, 'target_genome_index.txt'), collapse='/')
write.table(tbl.j2, outFile, sep='\t', quote=F, row.names=F, col.names=F)

Plotting community abundance distribution of target genomes


In [85]:
%%R -w 900 -h 350

ggplot(tbl.j2, aes(rank, rel_abund_perc)) +
    geom_point(size=3, shape='O', color='red') +
    labs(x='Rank', y='% relative abundance', title='Priming experiment community abundance distribution') +
    theme_bw() +
    theme(
        text = element_text(size=16)
        )


Simulating fragments of genomes that match priming_exp bulk OTUs


In [86]:
!cd $workDir; \
    SIPSim fragments \
    target_genome_index.txt \
    --fp $genomeDir \
    --fr $primerFile \
    --fld skewed-normal,9000,2500,-5 \
    --flr None,None \
    --nf 10000 \
    --np $nprocs \
    2> ampFrags.log \
    > ampFrags.pkl

Appending fragments from randomly selected genomes of total dataset (n=1210)

  • This is to obtain the richness of the bulk soil community
  • Random OTUs will be named after non-target OTUs in comm file

Making list of non-target OTUs


In [87]:
%%R -i workDir
# loading files

## target genome index (just OTUs with associated genome)
inFile = paste(c(workDir, 'target_genome_index.txt'), collapse='/')
tbl.target = read.delim(inFile, sep='\t', header=F)
colnames(tbl.target) = c('OTUId', 'fasta_file', 'genome_name')

## comm file of total community OTUs 
commFile = paste(c(workDir, 'comm.txt'), collapse='/')
tbl.comm = read.delim(commFile, sep='\t')

In [88]:
%%R
# just OTUs w/out an associated genome
tbl.j = anti_join(tbl.comm, tbl.target, c('taxon_name' = 'OTUId'))
n.nontarget.genomes = tbl.j$taxon_name %>% length
cat('Number of non-target genomes: ', n.nontarget.genomes, '\n')
cat('---------\n')
tbl.j %>% head(n=5)


Number of non-target genomes:  6408 
---------
  library taxon_name rel_abund_perc rank
1       1   OTU.9280   0.0008491831 6606
2       1   OTU.8991   0.0008491831 6605
3       1   OTU.8467   0.0008491831 6604
4       1   OTU.7687   0.0008491831 6603
5       1   OTU.7201   0.0008491831 6602

In [89]:
%%R -i comm_richness
# checking assumptions
cat('Target + nonTarget richness = total community richness?: ',
    n.target.genomes + n.nontarget.genomes == comm_richness, '\n')


Target + nonTarget richness = total community richness?:  TRUE 

In [90]:
%%R -i workDir
# writing out non-target OTU file
outFile = paste(c(workDir, 'comm_nonTarget.txt'), collapse='/')
write.table(tbl.j, outFile, sep='\t', quote=F, row.names=F)

Randomly selecting amplicon fragment length-GC KDEs from total genome pool


In [91]:
# List of non-target OTUs
inFile = os.path.join(workDir, 'comm_nonTarget.txt')
nonTarget = pd.read_csv(inFile, sep='\t')['taxon_name'].tolist()

print 'Number of non-target OTUs: {}'.format(len(nonTarget))
nonTarget[:4]


Number of non-target OTUs: 6408
Out[91]:
['OTU.9280', 'OTU.8991', 'OTU.8467', 'OTU.7687']

In [92]:
# loading amplicon fragments from full genome KDE dataset
inFile = os.path.join(workDir, 'ampFrags.pkl')
ampFrag_target = []
with open(inFile, 'rb') as iFH:
    ampFrag_target = pickle.load(iFH)
print 'Target OTU richness: {}'.format(len(ampFrag_target))


Target OTU richness: 198

In [93]:
# loading amplicon fragments from full genome KDE dataset
ampFrag_all = []
with open(allAmpFrags, 'rb') as iFH:
    ampFrag_all = pickle.load(iFH)
print 'Count of frag-GC KDEs for all genomes: {}'.format(len(ampFrag_all))


Count of frag-GC KDEs for all genomes: 1210

In [94]:
# random selection from list
#target_richness = len(ampFrag_target)

target_richness = len(ampFrag_target)
richness_needed = comm_richness - target_richness
print 'Number of random taxa needed to reach richness: {}'.format(richness_needed)

if richness_needed > 0:
    index = range(target_richness)
    index = np.random.choice(index, richness_needed)
    
    ampFrag_rand = []
    for i in index:
        sys.stderr.write('{},'.format(i))
        ampFrag_rand.append(copy.deepcopy(ampFrag_all[i]))
else:
    ampFrag_rand = []


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68,160,171,56,150,129,141,18,6,95,44,195,163,82,92,14,81,114,32,133,0,42,62,104,68,157,145,90,168,122,191,181,160,117,188,13,188,65,72,114,77,163,156,194,55,124,76,197,83,138,78,100,168,27,20,68,49,62,108,25,162,20,173,167,25,56,9,104,24,66,74,43,122,80,173,151,134,63,42,142,120,139,46,189,183,137,45,15,20,29,149,31,69,156,90,88,135,128,37,128,118,171,51,31,4,155,188,107,95,24,161,127,167,80,28,12,102,83,22,49,14,129,37,160,137,65,173,105,142,112,192,187,194,45,7,192,139,165,114,8,180,55,79,28,106,7,153,12,3,97,191,50,73,29,186,3,119,107,137,21,31,86,3,162,173,12,81,161,127,30,3,84,60,51,6,170,104,24,168,132,32,66,159,194,64,184,122,113,30,25,78,136,17,156,150,115,73,108,41,197,180,115,29,78,168,69,114,125,160,46,170,57,117,195,151,73,3,180,28,146,47,151,7,94,165,54,38,24,62,64,4,34,12,89,17,167,14,142,120,161,65,154,63,104,137,196,136,168,165,29,190,192,166,69,101,197,66,27,134,27,57,95,102,41,170,61,109,166,78,145,146,43,146,21,96,28,158,41,142,169,174,16,15,187,193,38,188,63,174,37,102,139,156,183,188,174,19,126,194,55,194,183,187,118,194,113,23,81,193,143,14,111,135,11,40,2,114,4,123,147,89,31,50,9,197,141,49,26,107,55,121,139,49,79,27,72,164,32,142,111,140,164,55,19,152,35,16,2,193,166,140,16,102,154,103,9,16,58,191,180,2,48,105,38,183,185,28,100,85,16,51,106,15,79,152,6,151,146,99,2,26,138,41,195,196,151,113,174,60,108,194,90,145,58,177,140,151,34,68,6,112,32,128,87,18,72,40,8,124,171,35,135,96,144,141,66,157,33,114,103,110,171,110,155,19,171,126,136,35,160,69,167,98,173,136,67,121,107,144,10,16,17,160,161,54,153,106,20,166,46,36,20,170,133,92,170,92,184,83,96,18,149,128,58,147,143,96,176,90,132,22,33,78,142,68,127,9,181,0,139,89,26,96,81,165,103,5,58,175,105,63,67,193,96,156,167,139,63,59,55,39,43,126,21,152,130,49,33,30,105,143,75,159,79,189,167,86,131,85,103,21,141,27,79,146,94,116,19,170,120,116,154,149,19,83,161,79,2,108,170,109,13,13,98,153,145,104,152,107,52,171,180,152,88,6,183,32,188,85,172,8,101,112,16,81,52,190,18,132,100,6,52,179,104,68,196,115,101,125,144,190,141,15,117,88,52,168,75,172,34,126,125,87,58,98,77,6,17,139,103,16,110,20,186,98,165,37,69,182,43,75,9,125,144,0,109,39,174,23,194,124,167,183,155,82,149,146,17,65,173,62,106,183,48,164,58,165,59,95,102,124,186,174,46,47,33,105,140,81,93,48,180,109,155,55,167,48,195,188,42,167,49,17,74,140,86,178,56,49,4,141,106,10,107,81,145,77,77,63,24,130,51,193,122,16,97,177,197,142,72,27,19,88,31,41,66,124,42,121,162,103,113,123,84,168,70,42,15,74,31,44,59,137,152,8,29,153,131,184,176,95,168,180,166,141,104,65,184,17,59,128,43,192,31,93,132,37,83,5,138,76,96,144,34,19,49,25,43,146,47,106,15,35,76,111,110,8,164,36,84,142,59,178,98,146,18,173,183,76,130,188,0,106,141,78,114,122,38,44,22,116,141,190,128,138,82,105,169,54,174,60,31,154,133,18,18,34,49,150,140,117,150,192,124,46,192,58,13,148,49,117,96,147,158,175,187,108,10,196,85,175,117,50,134,148,45,161,46,131,125,174,114,14,63,51,70,76,164,105,58,84,126,49,38,46,19,42,158,99,68,43,98,56,171,184,117,33,104,169,190,40,119,78,2,143,52,80,161,114,176,135,151,4,6,64,16,4,89,62,87,43,165,123,29,15,19,106,94,159,107,18,115,175,170,7,177,114,32,191,179,152,24,140,172,58,85,173,57,154,0,131,165,48,156,122,58,73,196,154,16,26,177,127,127,21,91,158,51,78,85,122,126,189,134,131,33,34,55,26,158,112,0,92,34,190,8,18,165,24,0,150,153,121,58,47,188,99,186,28,30,86,54,87,134,79,48,54,152,17,12,125,110,100,146,26,130,185,33,42,38,149,67,192,123,83,123,149,73,0,132,58,173,81,154,137,6,54,20,160,32,178,137,119,197,15,40,99,131,134,183,59,114,25,120,90,168,4,15,102,69,195,57,108,80,143,42,104,115,148,141,99,130,175,52,194,8,123,61,120,48,13,131,33,196,141,29,159,140,61,17,169,86,94,1,3,34,22,94,130,190,197,176,193,169,45,60,152,116,20,73,164,193,126,125,146,91,144,184,94,8,142,39,42,60,58,80,131,60,93,73,96,174,127,154,27,140,50,117,116,29,23,99,31,5,36,158,97,111,44,145,11,37,100,75,115,121,9,116,151,4,18,44,10,5,48,77,38,51,32,29,9,154,20,112,63,69,82,34,48,112,159,51,63,121,27,184,172,192,21,154,103,47,96,119,133,17,165,93,39,184,182,41,85,134,158,165,57,182,55,79,84,51,98,134,37,126,137,84,53,5,166,19,103,8,194,128,113,58,190,80,16,81,22,62,117,127,39,64,140,22,184,97,149,120,58,185,130,147,192,123,179,183,181,48,155,133,114,65,102,181,38,108,125,97,132,163,28,55,113,74,22,129,1,101,100,5,109,175,43,91,40,45,116,158,187,93,39,95,171,155,35,135,34,72,111,125,115,25,177,92,13,146,132,122,157,117,40,50,69,92,86,174,170,142,189,34,102,89,19,196,2,184,65,3,88,75,184,53,29,63,140,20,21,97,7,131,101,123,43,177,125,42,125,197,175,195,2,104,2,15,51,36,37,0,139,179,2,151,43,115,60,36,183,73,184,22,119,87,194,53,90,67,5,110,29,121,2,3,94,131,97,68,7,47,26,60,157,23,103,27,71,45,79,194,184,156,165,82,191,196,177,107,154,154,129,142,157,114,55,89,68,107,37,47,18,184,65,155,133,86,196,28,65,125,96,32,86,109,135,134,151,156,90,15,194,191,92,58,153,123,139,28,132,20,146,55,148,93,107,174,193,192,115,95,32,93,29,46,115,98,175,72,112,55,115,177,124,71,0,5,165,65,138,177,96,54,36,125,86,57,1,79,108,27,92,45,87,93,146,43,130,72,46,114,11,31,11,22,15,182,157,142,179,147,145,0,92,113,54,2,12,8,147,5,178,42,11,57,25,17,7,109,136,94,169,122,152,39,84,136,38,149,153,35,192,78,44,177,158,185,197,158,30,32,143,44,67,159,39,51,49,155,102,95,112,146,87,31,53,125,4,116,3,80,185,178,131,72,131,182,65,101,127,165,27,35,63,6,159,181,56,156,34,124,57,158,145,122,142,155,56,122,20,42,4,10,6,155,197,59,105,101,61,145,116,52,117,172,98,171,84,68,65,131,54,22,97,1,91,125,59,187,47,69,172,188,96,77,17,20,74,94,104,48,127,22,122,178,80,150,30,5,101,178,105,147,140,22,19,63,113,50,153,182,179,150,114,139,132,131,139,21,4,3,40,68,22,0,17,126,31,11,36,140,17,111,144,187,130,96,24,158,78,54,66,14,54,174,32,106,88,45,116,107,133,28,164,151,32,183,55,46,62,22,102,74,18,16,99,101,34,124,148,67,171,171,38,41,87,168,24,100,36,164,134,53,113,136,129,80,197,133,133,154,35,73,1,133,38,8,39,88,54,127,145,85,29,16,110,100,139,194,94,66,43,61,43,41,171,156,3,118,138,106,101,103,51,75,97,163,181,120,47,53,101,189,182,25,40,145,90,75,39,31,129,129,78,159,154,196,152,194,137,189,178,21,121,127,87,36,124,182,60,109,95,101,83,8,131,73,109,43,69,190,150,150,138,156,153,177,195,40,137,110,9,82,95,63,185,17,111,159,130,156,106,180,194,134,18,147,7,20,4,95,64,191,61,36,54,101,82,30,151,148,28,95,93,91,54,69,150,136,45,107,31,148,62,13,140,111,196,141,51,13,4,15,82,14,103,43,148,124,158,60,48,136,112,162,78,197,132,113,42,98,143,112,134,22,16,42,28,159,108,123,12,146,8,86,157,99,152,51,173,113,165,177,162,30,157,160,22,160,179,141,166,126,147,39,145,185,110,138,38,121,118,117,65,62,177,165,89,70,143,81,92,104,160,22,136,157,67,185,67,151,72,194,58,4,77,186,157,15,149,133,51,152,88,118,102,8,31,134,85,188,80,105,173,33,86,121,50,149,24,79,176,83,86,127,42,56,24,141,63,2,21,40,187,49,98,9,58,24,76,130,73,136,113,11,74,77,88,63,3,73,86,178,176,73,49,135,112,129,138,182,26,167,109,62,123,148,138,50,44,188,127,8,109,32,195,103,7,21,38,188,16,16,101,119,36,61,22,140,22,71,146,17,19,74,1,30,91,181,157,59,68,76,11,152,154,47,87,150,12,128,177,184,145,19,146,170,176,139,109,70,21,9,123,73,86,34,105,28,112,56,161,127,79,43,127,69,10,103,91,104,26,103,194,47,46,60,110,33,
Number of random taxa needed to reach richness: 6408

In [95]:
# renaming randomly selected KDEs by non-target OTU-ID
for i in range(len(ampFrag_rand)):
    ampFrag_rand[i][0] = nonTarget[i]

In [96]:
# appending random taxa to target taxa and writing
outFile = os.path.join(workDir, 'ampFrags_wRand.pkl')

with open(outFile, 'wb') as oFH:
    x = ampFrag_target + ampFrag_rand
    print 'Number of taxa in output: {}'.format(len(x))
    pickle.dump(x, oFH)


Number of taxa in output: 6606

Converting fragments to kde object


In [97]:
!cd $workDir; \
    SIPSim fragment_kde \
    ampFrags_wRand.pkl \
    > ampFrags_wRand_kde.pkl

Adding diffusion


In [98]:
!cd $workDir; \
    SIPSim diffusion \
    ampFrags_wRand_kde.pkl \
    --np $nprocs \
    > ampFrags_wRand_kde_dif.pkl


Processing: OTU.759
Processing: OTU.3200
Processing: OTU.417
Processing: OTU.4687
Processing: OTU.6773
Processing: OTU.2002
Processing: OTU.507
Processing: OTU.9232
Processing: OTU.142
Processing: OTU.5335
Processing: OTU.4684
Processing: OTU.757
Processing: OTU.12933
Processing: OTU.2003
Processing: OTU.504
Processing: OTU.505
Processing: OTU.6236
Processing: OTU.411
Processing: OTU.8214
Processing: OTU.1294
Processing: OTU.4685
Processing: OTU.1969
Processing: OTU.13575
Processing: OTU.4398
Processing: OTU.4929
Processing: OTU.502
Processing: OTU.6231
Processing: OTU.4928
Processing: OTU.412
Processing: OTU.5337
Processing: OTU.7608
Processing: OTU.2807
Processing: OTU.4683
Processing: OTU.12668
Processing: OTU.13576
Processing: OTU.6722
Processing: OTU.6147
Processing: OTU.839
Processing: OTU.503
Processing: OTU.6230
Processing: OTU.13948
Processing: OTU.1308
Processing: OTU.4229
Processing: OTU.4814
Processing: OTU.8216
Processing: OTU.9278
Processing: OTU.933
Processing: OTU.4680
Processing: OTU.5555
Processing: OTU.12666
Processing: OTU.7874
Processing: OTU.6721
Processing: OTU.6146
Processing: OTU.273
Processing: OTU.2006
Processing: OTU.500
Processing: OTU.6233
Processing: OTU.3604
Processing: OTU.13941
Processing: OTU.4224
Processing: OTU.3014
Processing: OTU.4996
Processing: OTU.7642
Processing: OTU.6959
Processing: OTU.932
Processing: OTU.4681
Processing: OTU.5554
Processing: OTU.5557
Processing: OTU.1965
Processing: OTU.7876
Processing: OTU.6335
Processing: OTU.6727
Processing: OTU.3425
Processing: OTU.274
Processing: OTU.2007
Processing: OTU.501
Processing: OTU.1776
Processing: OTU.7048
Processing: OTU.13942
Processing: OTU.1305
Processing: OTU.1745
Processing: OTU.3155
Processing: OTU.11627
Processing: OTU.1176
Processing: OTU.931
Processing: OTU.7816
Processing: OTU.7817
Processing: OTU.2276
Processing: OTU.12664
Processing: OTU.7872
Processing: OTU.1524
Processing: OTU.9046
Processing: OTU.3424
Processing: OTU.275
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Making an incorp config file


In [99]:
!cd $workDir; \
    SIPSim incorpConfigExample \
    --percTaxa 0 \
    --percIncorpUnif 100 \
    > PT0_PI100.config

Adding isotope incorporation to BD distribution


In [100]:
!cd $workDir; \
    SIPSim isotope_incorp \
    ampFrags_wRand_kde_dif.pkl \
    PT0_PI100.config \
    --comm comm.txt \
    --np $nprocs \
    > ampFrags_wRand_kde_dif_incorp.pkl


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Calculating BD shift from isotope incorporation


In [101]:
!cd $workDir; \
    SIPSim BD_shift \
    ampFrags_wRand_kde_dif.pkl \
    ampFrags_wRand_kde_dif_incorp.pkl \
    --np $nprocs \
    > ampFrags_wRand_kde_dif_incorp_BD-shift.txt


Loading KDE objects...
Calculating BD shifts...
  Comparing libraries; "NA", "1"
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  Comparing libraries; "NA", "2"
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  Processing: OTU.440
  Processing: OTU.2453
  Processing: OTU.7931
  Processing: OTU.661
  Processing: OTU.3504
  Processing: OTU.1350
  Processing: OTU.3899
  Processing: OTU.59
  Processing: OTU.6444
  Processing: OTU.468
  Processing: OTU.3856
  Processing: OTU.5820
  Processing: OTU.8194
  Processing: OTU.1394
  Processing: OTU.1548
  Processing: OTU.447
  Processing: OTU.7933
  Processing: OTU.2459
  Processing: OTU.12291
  Processing: OTU.9432
  Processing: OTU.2479
  Processing: OTU.1357
  Processing: OTU.1003
  Processing: OTU.3857
  Processing: OTU.2700
  Processing: OTU.5823
  Processing: OTU.8199
  Processing: OTU.1393
  Processing: OTU.446
  Processing: OTU.1546
  Processing: OTU.2458
  Processing: OTU.12290
  Processing: OTU.3306
  Processing: OTU.2477
  Processing: OTU.464
  Processing: OTU.8502
  Processing: OTU.3854
  Processing: OTU.1356
  Processing: OTU.1002
  Processing: OTU.6130
  Processing: OTU.9379
  Processing: OTU.1392
  Processing: OTU.113
  Processing: OTU.12296
  Processing: OTU.1906
  Processing: OTU.1544
  Processing: OTU.467
  Processing: OTU.5825
  Processing: OTU.3855
  Processing: OTU.4275
  Processing: OTU.8991
  Processing: OTU.1001
  Processing: OTU.3965
  Processing: OTU.1391
  Processing: OTU.12295
  Processing: OTU.12299
  Processing: OTU.444
  Processing: OTU.1907
  Processing: OTU.4106
  Processing: OTU.2474
  Processing: OTU.5827
  Processing: OTU.8996
  Processing: OTU.3853
  Processing: OTU.1354
  Processing: OTU.2251
  Processing: OTU.1000
  Processing: OTU.1390
  Processing: OTU.6123
  Processing: OTU.2411
  Processing: OTU.1904
  Processing: OTU.1542
  Processing: OTU.5826
  Processing: OTU.8997
  Processing: OTU.3850
  Processing: OTU.4279
  Processing: OTU.6442
  Processing: OTU.3892
  Processing: OTU.660
  Processing: OTU.1399
  Processing: OTU.2410
  Processing: OTU.1905
  Processing: OTU.2837
  Processing: OTU.1543
  Processing: OTU.7748
  Processing: OTU.3851
  Processing: OTU.1358
  Processing: OTU.12089
  Processing: OTU.3893
  Processing: OTU.692
  Processing: OTU.1398
  Processing: OTU.2413
  Processing: OTU.1902
  Processing: OTU.2836
  Processing: OTU.2834
  Processing: OTU.7749
  Processing: OTU.1540
  Processing: OTU.3858
  Processing: OTU.6810
  Processing: OTU.6089
  Processing: OTU.3890
  Processing: OTU.921
  Processing: OTU.690
  Processing: OTU.3739
  Processing: OTU.2412
  Processing: OTU.2415
  Processing: OTU.1903
  Processing: OTU.2833
  Processing: OTU.7741
  Processing: OTU.3859
  Processing: OTU.1541
  Processing: OTU.3655
  Processing: OTU.6813
  Processing: OTU.4758
  Processing: OTU.6087
  Processing: OTU.3891
  Processing: OTU.3738
  Processing: OTU.2414
  Processing: OTU.2832
  Processing: OTU.1900
  Processing: OTU.7746
  Processing: OTU.46
  Processing: OTU.691
  Processing: OTU.6817
  Processing: OTU.3526
  Processing: OTU.6085
  Processing: OTU.3896
  Processing: OTU.3897
  Processing: OTU.3735
  Processing: OTU.2831
  Processing: OTU.2417
  Processing: OTU.2416
  Processing: OTU.1908
  Processing: OTU.7745
  Processing: OTU.4938
  Processing: OTU.924
  Processing: OTU.6816
  Processing: OTU.3894
  Processing: OTU.3035
  Processing: OTU.3734
  Processing: OTU.2830
  Processing: OTU.1909
  Processing: OTU.4298
  Processing: OTU.6112
  Processing: OTU.6819
  Processing: OTU.3895
  Processing: OTU.3036
  Processing: OTU.3733
  Processing: OTU.10355
  Processing: OTU.1920
  Processing: OTU.4294
  Processing: OTU.4296
  Processing: OTU.280
  Processing: OTU.6818
  Processing: OTU.13458
  Processing: OTU.3525
  Processing: OTU.1130
  Processing: OTU.4557
  Processing: OTU.4291
  Processing: OTU.1585
  Processing: OTU.43
  Processing: OTU.4572
  Processing: OTU.13104
  Processing: OTU.6002
  Processing: OTU.2839
  Processing: OTU.4658
  Processing: OTU.4290
  Processing: OTU.6648
  Processing: OTU.9164
  Processing: OTU.4575
  Processing: OTU.3523
  Processing: OTU.4247
  Processing: OTU.5591
  Processing: OTU.5590
  Processing: OTU.4292
  Processing: OTU.829
  Processing: OTU.1689
  Processing: OTU.3520
  Processing: OTU.4244
  Processing: OTU.5593
  Processing: OTU.568
  Processing: OTU.2112
  Processing: OTU.1688
  Processing: OTU.3033
  Processing: OTU.4653
  Processing: OTU.6838
  Processing: OTU.5597
  Processing: OTU.6642
  Processing: OTU.1056
  Processing: OTU.3038
  Processing: OTU.4245
  Processing: OTU.5596
  Processing: OTU.5598
  Processing: OTU.828
  Processing: OTU.1681
  Processing: OTU.3039
  Processing: OTU.1362
  Processing: OTU.12603
  Processing: OTU.5721
  Processing: OTU.1680
  Processing: OTU.1137
  Processing: OTU.6008
  Processing: OTU.12604
  Processing: OTU.2039
  Processing: OTU.1683
  Processing: OTU.6071
  Processing: OTU.5987
  Processing: OTU.8820
  Processing: OTU.538
  Processing: OTU.1682
  Processing: OTU.1363
  Processing: OTU.7236
  Processing: OTU.13808
  Processing: OTU.13806
  Processing: OTU.2115
  Processing: OTU.1685
  Processing: OTU.3978
  Processing: OTU.7237
  Processing: OTU.13801
  Processing: OTU.825
  Processing: OTU.1684
  Processing: OTU.8764
  Processing: OTU.7233
  Processing: OTU.5047
  Processing: OTU.1686
  Processing: OTU.5724
  Processing: OTU.4241
  Processing: OTU.7230
  Processing: OTU.5046
  Processing: OTU.5575
  Processing: OTU.288
  Processing: OTU.7238
  Processing: OTU.5045
  Processing: OTU.7788
  Processing: OTU.4932
  Processing: OTU.4933
  Processing: OTU.2033
  Processing: OTU.7239
  Processing: OTU.5044
  Processing: OTU.3269
  Processing: OTU.293
  Processing: OTU.5042
  Processing: OTU.8468
  Processing: OTU.3268
  Processing: OTU.4935
  Processing: OTU.5041
  Processing: OTU.2031
  Processing: OTU.3261
  Processing: OTU.5040
  Processing: OTU.1057
  Processing: OTU.3260
  Processing: OTU.530
  Processing: OTU.3527
  Processing: OTU.3524
  Processing: OTU.3264
  Processing: OTU.3037
  Processing: OTU.14148
  Processing: OTU.3267
  Processing: OTU.3522
  Processing: OTU.3266
  Processing: OTU.14140
  Processing: OTU.810
  Processing: OTU.811
  Processing: OTU.14142
  Processing: OTU.9789
  Processing: OTU.812
  Processing: OTU.11643
  Processing: OTU.813
  Processing: OTU.814
  Processing: OTU.11642
  Processing: OTU.815
  Processing: OTU.3032
  Processing: OTU.9782
  Processing: OTU.816
  Processing: OTU.6001
  Processing: OTU.817
  Processing: OTU.9785
  Processing: OTU.818
  Processing: OTU.4429
  Processing: OTU.819
  Processing: OTU.2819
  Processing: OTU.2027
  Processing: OTU.2818
  Processing: OTU.2020
  Processing: OTU.5849
  Processing: OTU.5848
  Processing: OTU.2022
  Processing: OTU.2023
  Processing: OTU.5572
  Processing: OTU.3198
  Processing: OTU.3194
  Processing: OTU.3192
  Processing: OTU.3191
  Processing: OTU.3190
  Processing: OTU.5691
  Processing: OTU.5696
  Processing: OTU.728

Simulating gradient fractions


In [102]:
!cd $workDir; \
    SIPSim gradient_fractions \
    comm.txt \
    > fracs.txt

Simulating an OTU table


In [103]:
!cd $workDir; \
    SIPSim OTU_table \
    ampFrags_wRand_kde_dif_incorp.pkl \
    comm.txt \
    fracs.txt \
    --abs 1e9 \
    --np $nprocs \
    > OTU_abs1e9.txt


Loading files...
Simulating OTUs...
Processing library: "1"
  Processing taxon: "OTU.1"
   taxon abs-abundance:  31948911
  Processing taxon: "OTU.159"
   taxon abs-abundance:  1923768
  Processing taxon: "OTU.129"
   taxon abs-abundance:  1064994
  Processing taxon: "OTU.98"
   taxon abs-abundance:  740069
  Processing taxon: "OTU.270"
   taxon abs-abundance:  546083
  Processing taxon: "OTU.1528"
   taxon abs-abundance:  1057472
  Processing taxon: "OTU.5914"
   taxon abs-abundance:  739619
  Processing taxon: "OTU.101"
   taxon abs-abundance:  1898287
  Processing taxon: "OTU.177"
   taxon abs-abundance:  423454
  Processing taxon: "OTU.6767"
   taxon abs-abundance:  545438
  Processing taxon: "OTU.8004"
   taxon abs-abundance:  422768
  Processing taxon: "OTU.289"
   taxon abs-abundance:  739004
  Processing taxon: "OTU.5917"
   taxon abs-abundance:  334173
  Processing taxon: "OTU.386"
   taxon abs-abundance:  544468
  Processing taxon: "OTU.843"
   taxon abs-abundance:  1046772
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.421"
   taxon abs-abundance:  1042147
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.6187"
   taxon abs-abundance:  1034847
  Processing taxon: "OTU.1010"
   taxon abs-abundance:  422418
  Processing taxon: "OTU.1128"
   taxon abs-abundance:  333473
  Processing taxon: "OTU.3332"
   taxon abs-abundance:  279193
  Processing taxon: "OTU.4707"
   taxon abs-abundance:  544419
  Processing taxon: "OTU.172"
   taxon abs-abundance:  737323
  Processing taxon: "OTU.1814"
   taxon abs-abundance:  332893
  Processing taxon: "OTU.369"
   taxon abs-abundance:  421313
  Processing taxon: "OTU.3477"
   taxon abs-abundance:  277939
  Processing taxon: "OTU.616"
   taxon abs-abundance:  331969
  Processing taxon: "OTU.2144"
   taxon abs-abundance:  228531
  Processing taxon: "OTU.878"
   taxon abs-abundance:  276921
  Processing taxon: "OTU.6450"
  Processing taxon: "OTU.550"
   taxon abs-abundance:  420623
   taxon abs-abundance:  541256
  Processing taxon: "OTU.5241"
   taxon abs-abundance:  1030925
  Processing taxon: "OTU.16"
   taxon abs-abundance:  1892173
  Processing taxon: "OTU.8003"
   taxon abs-abundance:  228474
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.373"
   taxon abs-abundance:  227358
  Processing taxon: "OTU.323"
   taxon abs-abundance:  331647
  Processing taxon: "OTU.8842"
   taxon abs-abundance:  276817
  Processing taxon: "OTU.179"
   taxon abs-abundance:  731121
  Processing taxon: "OTU.2530"
   taxon abs-abundance:  226790
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.13701"
   taxon abs-abundance:  226086
  Processing taxon: "OTU.3358"
   taxon abs-abundance:  420354
  Processing taxon: "OTU.669"
   taxon abs-abundance:  197093
  Processing taxon: "OTU.542"
  Processing taxon: "OTU.6407"
   taxon abs-abundance:  275955
   taxon abs-abundance:  539895
  Processing taxon: "OTU.233"
   taxon abs-abundance:  331479
  Processing taxon: "OTU.140"
   taxon abs-abundance:  225650
  Processing taxon: "OTU.2372"
   taxon abs-abundance:  196859
  Processing taxon: "OTU.1638"
   taxon abs-abundance:  275383
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.4450"
   taxon abs-abundance:  275053
  Processing taxon: "OTU.190"
   taxon abs-abundance:  418159
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.714"
   taxon abs-abundance:  417476
  Processing taxon: "OTU.709"
  Processing taxon: "OTU.398"
   taxon abs-abundance:  196831
   taxon abs-abundance:  225603
  Processing taxon: "OTU.103"
   taxon abs-abundance:  331210
  Processing taxon: "OTU.504"
   taxon abs-abundance:  170649
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.732"
   taxon abs-abundance:  170568
  Processing taxon: "OTU.4467"
   taxon abs-abundance:  728520
  Processing taxon: "OTU.501"
   taxon abs-abundance:  1024914
  Processing taxon: "OTU.539"
   taxon abs-abundance:  538902
  Processing taxon: "OTU.192"
   taxon abs-abundance:  196204
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.383"
   taxon abs-abundance:  195414
  Processing taxon: "OTU.1412"
   taxon abs-abundance:  274889
  Processing taxon: "OTU.4996"
   taxon abs-abundance:  225502
  Processing taxon: "OTU.509"
   taxon abs-abundance:  170467
  Processing taxon: "OTU.419"
   taxon abs-abundance:  330075
  Processing taxon: "OTU.170"
   taxon abs-abundance:  416339
  Processing taxon: "OTU.530"
   taxon abs-abundance:  195048
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.473"
   taxon abs-abundance:  195037
  Processing taxon: "OTU.870"
   taxon abs-abundance:  224736
  Processing taxon: "OTU.2923"
   taxon abs-abundance:  170331
  Processing taxon: "OTU.381"
   taxon abs-abundance:  274713
  Processing taxon: "OTU.1034"
   taxon abs-abundance:  194920
  Processing taxon: "OTU.414"
  Processing taxon: "OTU.6102"
   taxon abs-abundance:  170188
   taxon abs-abundance:  151696
  Processing taxon: "OTU.748"
  Processing taxon: "OTU.3062"
   taxon abs-abundance:  328671
   taxon abs-abundance:  224448
  Processing taxon: "OTU.11322"
   taxon abs-abundance:  536823
  Processing taxon: "OTU.371"
   taxon abs-abundance:  272221
  Processing taxon: "OTU.8941"
  Processing taxon: "OTU.707"
   taxon abs-abundance:  151691
  Processing taxon: "OTU.3841"
   taxon abs-abundance:  414378
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.9954"
   taxon abs-abundance:  194736
   taxon abs-abundance:  413950
  Processing taxon: "OTU.984"
   taxon abs-abundance:  170154
  Processing taxon: "OTU.153"
   taxon abs-abundance:  724724
  Processing taxon: "OTU.305"
   taxon abs-abundance:  224168
  Processing taxon: "OTU.7834"
   taxon abs-abundance:  151285
  Processing taxon: "OTU.841"
   taxon abs-abundance:  170100
  Processing taxon: "OTU.316"
  Processing taxon: "OTU.231"
   taxon abs-abundance:  327705
   taxon abs-abundance:  194616
  Processing taxon: "OTU.144"
   taxon abs-abundance:  272065
  Processing taxon: "OTU.76"
   taxon abs-abundance:  1879774
  Processing taxon: "OTU.985"
   taxon abs-abundance:  151270
  Processing taxon: "OTU.453"
   taxon abs-abundance:  224066
  Processing taxon: "OTU.7337"
   taxon abs-abundance:  169724
  Processing taxon: "OTU.1127"
   taxon abs-abundance:  132239
  Processing taxon: "OTU.241"
   taxon abs-abundance:  1022172
  Processing taxon: "OTU.717"
   taxon abs-abundance:  194086
  Processing taxon: "OTU.3519"
   taxon abs-abundance:  412996
  Processing taxon: "OTU.317"
  Processing taxon: "OTU.758"
   taxon abs-abundance:  531582
   taxon abs-abundance:  151028
  Processing taxon: "OTU.474"
   taxon abs-abundance:  271944
  Processing taxon: "OTU.794"
   taxon abs-abundance:  132066
  Processing taxon: "OTU.284"
   taxon abs-abundance:  169661
  Processing taxon: "OTU.399"
   taxon abs-abundance:  326985
  Processing taxon: "OTU.3355"
   taxon abs-abundance:  223749
  Processing taxon: "OTU.449"
   taxon abs-abundance:  194033
  Processing taxon: "OTU.13643"
   taxon abs-abundance:  150979
  Processing taxon: "OTU.900"
   taxon abs-abundance:  132032
  Processing taxon: "OTU.1689"
   taxon abs-abundance:  169591
  Processing taxon: "OTU.664"
   taxon abs-abundance:  150977
  Processing taxon: "OTU.208"
  Processing taxon: "OTU.658"
   taxon abs-abundance:  271514
  Processing taxon: "OTU.123"
   taxon abs-abundance:  131880
   taxon abs-abundance:  721248
  Processing taxon: "OTU.2233"
  Processing taxon: "OTU.1292"
   taxon abs-abundance:  223570
   taxon abs-abundance:  193871
  Processing taxon: "OTU.682"
   taxon abs-abundance:  412719
  Processing taxon: "OTU.478"
   taxon abs-abundance:  326510
  Processing taxon: "OTU.12647"
   taxon abs-abundance:  169123
  Processing taxon: "OTU.4715"
   taxon abs-abundance:  116325
  Processing taxon: "OTU.2347"
  Processing taxon: "OTU.853"
   taxon abs-abundance:  131723
   taxon abs-abundance:  150755
  Processing taxon: "OTU.3228"
   taxon abs-abundance:  531080
  Processing taxon: "OTU.402"
   taxon abs-abundance:  192793
  Processing taxon: "OTU.483"
  Processing taxon: "OTU.1702"
   taxon abs-abundance:  223235
   taxon abs-abundance:  116149
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.5904"
   taxon abs-abundance:  116074
  Processing taxon: "OTU.3817"
   taxon abs-abundance:  169046
  Processing taxon: "OTU.12448"
  Processing taxon: "OTU.4938"
   taxon abs-abundance:  131603
   taxon abs-abundance:  270909
  Processing taxon: "OTU.874"
   taxon abs-abundance:  150620
  Processing taxon: "OTU.2414"
   taxon abs-abundance:  116072
  Processing taxon: "OTU.9497"
   taxon abs-abundance:  326118
  Processing taxon: "OTU.648"
   taxon abs-abundance:  131501
  Processing taxon: "OTU.6783"
   taxon abs-abundance:  192664
  Processing taxon: "OTU.3886"
   taxon abs-abundance:  168198
  Processing taxon: "OTU.756"
   taxon abs-abundance:  149974
  Processing taxon: "OTU.274"
  Processing taxon: "OTU.637"
   taxon abs-abundance:  411621
   taxon abs-abundance:  222862
  Processing taxon: "OTU.6134"
   taxon abs-abundance:  115890
  Processing taxon: "OTU.8572"
   taxon abs-abundance:  130557
  Processing taxon: "OTU.331"
   taxon abs-abundance:  269637
  Processing taxon: "OTU.1489"
  Processing taxon: "OTU.3398"
   taxon abs-abundance:  149397
   taxon abs-abundance:  168102
  Processing taxon: "OTU.1270"
  Processing taxon: "OTU.2584"
   taxon abs-abundance:  115861
   taxon abs-abundance:  192547
  Processing taxon: "OTU.6875"
   taxon abs-abundance:  1020749
  Processing taxon: "OTU.298"
   taxon abs-abundance:  130251
  Processing taxon: "OTU.3083"
   taxon abs-abundance:  222767
  Processing taxon: "OTU.688"
  Processing taxon: "OTU.8067"
   taxon abs-abundance:  326086
  Processing taxon: "OTU.416"
   taxon abs-abundance:  529923
  Processing taxon: "OTU.5428"
   taxon abs-abundance:  115686
   taxon abs-abundance:  718679
  Processing taxon: "OTU.774"
   taxon abs-abundance:  149025
  Processing taxon: "OTU.5367"
   taxon abs-abundance:  168089
  Processing taxon: "OTU.515"
   taxon abs-abundance:  130213
  Processing taxon: "OTU.6192"
   taxon abs-abundance:  192208
  Processing taxon: "OTU.8712"
  Processing taxon: "OTU.395"
   taxon abs-abundance:  269255
   taxon abs-abundance:  105277
  Processing taxon: "OTU.350"
   taxon abs-abundance:  115645
  Processing taxon: "OTU.133"
   taxon abs-abundance:  407424
  Processing taxon: "OTU.254"
   taxon abs-abundance:  148885
  Processing taxon: "OTU.281"
   taxon abs-abundance:  222172
  Processing taxon: "OTU.2771"
  Processing taxon: "OTU.8534"
   taxon abs-abundance:  105258
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.12515"
   taxon abs-abundance:  130058
  Processing taxon: "OTU.394"
   taxon abs-abundance:  105040
   taxon abs-abundance:  168008
  Processing taxon: "OTU.973"
   taxon abs-abundance:  115352
  Processing taxon: "OTU.5294"
   taxon abs-abundance:  192072
  Processing taxon: "OTU.4617"
  Processing taxon: "OTU.460"
  Processing taxon: "OTU.683"
   taxon abs-abundance:  104922
   taxon abs-abundance:  325743
   taxon abs-abundance:  148781
  Processing taxon: "OTU.344"
   taxon abs-abundance:  129452
  Processing taxon: "OTU.426"
  Processing taxon: "OTU.689"
   taxon abs-abundance:  114983
   taxon abs-abundance:  269013
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   taxon abs-abundance:  121618
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  Processing taxon: "OTU.1063"
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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  Processing taxon: "OTU.4809"
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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  Processing taxon: "OTU.10787"
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   taxon abs-abundance:  39196
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   taxon abs-abundance:  39186
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   taxon abs-abundance:  38118
  Processing taxon: "OTU.1274"
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   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.13022"
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  Processing taxon: "OTU.5489"
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.8931"
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   taxon abs-abundance:  28390
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  Processing taxon: "OTU.1323"
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.3144"
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   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.4930"
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   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.2908"
   taxon abs-abundance:  29335
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  Processing taxon: "OTU.2521"
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   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.2906"
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   taxon abs-abundance:  24141
   WARNING: No bins for taxon; likely caused by no BD KDE
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   taxon abs-abundance:  24135
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   WARNING: No bins for taxon; likely caused by no BD KDE
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   taxon abs-abundance:  8492
  Processing taxon: "OTU.8218"
  Processing taxon: "OTU.8008"
  Processing taxon: "OTU.13652"
   taxon abs-abundance:  15840
   taxon abs-abundance:  15358
   taxon abs-abundance:  8492
  Processing taxon: "OTU.14258"
   taxon abs-abundance:  8492
  Processing taxon: "OTU.842"
  Processing taxon: "OTU.8159"
   taxon abs-abundance:  809204
   taxon abs-abundance:  15358
  Processing taxon: "OTU.2212"
   taxon abs-abundance:  8492
  Processing taxon: "OTU.8170"
  Processing taxon: "OTU.2937"
   taxon abs-abundance:  15358
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.9344"
   taxon abs-abundance:  8492
   taxon abs-abundance:  15358
  Processing taxon: "OTU.3558"
   taxon abs-abundance:  8492
  Processing taxon: "OTU.9674"
  Processing taxon: "OTU.4568"
   taxon abs-abundance:  15358
   taxon abs-abundance:  8492
  Processing taxon: "OTU.5042"
  Processing taxon: "OTU.9734"
   taxon abs-abundance:  8492
   taxon abs-abundance:  15358
  Processing taxon: "OTU.5400"
   taxon abs-abundance:  8492
  Processing taxon: "OTU.9979"
  Processing taxon: "OTU.5411"
   taxon abs-abundance:  15358
   taxon abs-abundance:  8492
  Processing taxon: "OTU.5835"
   taxon abs-abundance:  8492
  Processing taxon: "OTU.6280"
   taxon abs-abundance:  15292
  Processing taxon: "OTU.6109"
   taxon abs-abundance:  8492
  Processing taxon: "OTU.12101"
  Processing taxon: "OTU.6328"
   taxon abs-abundance:  15163
   taxon abs-abundance:  8492
  Processing taxon: "OTU.7201"
   taxon abs-abundance:  8492
  Processing taxon: "OTU.3567"
   taxon abs-abundance:  15163
  Processing taxon: "OTU.7687"
   taxon abs-abundance:  8492
  Processing taxon: "OTU.6708"
  Processing taxon: "OTU.8467"
   taxon abs-abundance:  14994
   taxon abs-abundance:  8492
  Processing taxon: "OTU.8991"
  Processing taxon: "OTU.3916"
   taxon abs-abundance:  8492
   taxon abs-abundance:  14981
  Processing taxon: "OTU.9280"
   taxon abs-abundance:  8492
  Processing taxon: "OTU.9802"
   taxon abs-abundance:  14922
  Processing taxon: "OTU.6370"
   taxon abs-abundance:  14861
  Processing taxon: "OTU.13695"
   taxon abs-abundance:  14846
  Processing taxon: "OTU.2957"
   taxon abs-abundance:  14772
  Processing taxon: "OTU.5646"
   taxon abs-abundance:  14737
  Processing taxon: "OTU.7202"
   taxon abs-abundance:  14696
  Processing taxon: "OTU.62"
   taxon abs-abundance:  1482588
  Processing taxon: "OTU.6795"
   taxon abs-abundance:  14618
  Processing taxon: "OTU.12519"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.13084"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.13763"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.2167"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.2983"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.3600"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.4389"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.4509"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.4585"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.4766"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.4998"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.5252"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.5259"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.5491"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.5659"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.6093"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.6250"
   taxon abs-abundance:  14486
  Processing taxon: "OTU.3156"
   taxon abs-abundance:  803471
  Processing taxon: "OTU.1856"
   taxon abs-abundance:  794252
  Processing taxon: "OTU.41"
   taxon abs-abundance:  1481080
  Processing taxon: "OTU.2147"
   taxon abs-abundance:  788266
  Processing taxon: "OTU.631"
   taxon abs-abundance:  785475
  Processing taxon: "OTU.67"
   taxon abs-abundance:  1462451
  Processing taxon: "OTU.150"
   taxon abs-abundance:  782769
  Processing taxon: "OTU.5714"
   taxon abs-abundance:  1452662
  Processing taxon: "OTU.7967"
   taxon abs-abundance:  777477
  Processing taxon: "OTU.225"
   taxon abs-abundance:  765178
  Processing taxon: "OTU.112"
   taxon abs-abundance:  1439713
  Processing taxon: "OTU.7866"
   taxon abs-abundance:  762122
  Processing taxon: "OTU.99"
   taxon abs-abundance:  760411
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.8359"
   taxon abs-abundance:  759740
  Processing taxon: "OTU.28"
   taxon abs-abundance:  1421994
  Processing taxon: "OTU.5845"
   taxon abs-abundance:  758760
  Processing taxon: "OTU.3"
   taxon abs-abundance:  10983385
  Processing taxon: "OTU.130"
   taxon abs-abundance:  755629
  Processing taxon: "OTU.66"
   taxon abs-abundance:  1421889
  Processing taxon: "OTU.3173"
   taxon abs-abundance:  754759
  Processing taxon: "OTU.405"
   taxon abs-abundance:  754409
  Processing taxon: "OTU.134"
   taxon abs-abundance:  1420131
  Processing taxon: "OTU.1759"
   taxon abs-abundance:  752058
  Processing taxon: "OTU.3368"
   taxon abs-abundance:  749385
  Processing taxon: "OTU.239"
   taxon abs-abundance:  1408744
  Processing taxon: "OTU.193"
   taxon abs-abundance:  748046
  Processing taxon: "OTU.155"
   taxon abs-abundance:  747494
  Processing taxon: "OTU.2944"
   taxon abs-abundance:  1408538
  Processing taxon: "OTU.185"
   taxon abs-abundance:  745613
  Processing taxon: "OTU.167"
   taxon abs-abundance:  743197
  Processing taxon: "OTU.125"
   taxon abs-abundance:  1403683
  Processing taxon: "OTU.5712"
   taxon abs-abundance:  741476
  Processing taxon: "OTU.1368"
   taxon abs-abundance:  741257
  Processing taxon: "OTU.221"
   taxon abs-abundance:  1398523
  Processing taxon: "OTU.93"
   taxon abs-abundance:  1393486
  Processing taxon: "OTU.1865"
   taxon abs-abundance:  1388873
  Processing taxon: "OTU.7"
   taxon abs-abundance:  10656666
  Processing taxon: "OTU.138"
   taxon abs-abundance:  1353820
  Processing taxon: "OTU.160"
   taxon abs-abundance:  1348218
  Processing taxon: "OTU.4663"
   taxon abs-abundance:  1342573
  Processing taxon: "OTU.70"
   taxon abs-abundance:  1341751
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.765"
   taxon abs-abundance:  1322300
  Processing taxon: "OTU.4038"
   taxon abs-abundance:  1320976
  Processing taxon: "OTU.7536"
   taxon abs-abundance:  1301721
  Processing taxon: "OTU.194"
   taxon abs-abundance:  1297857
  Processing taxon: "OTU.91"
   taxon abs-abundance:  1292588
  Processing taxon: "OTU.2"
   taxon abs-abundance:  10558499
  Processing taxon: "OTU.7788"
   taxon abs-abundance:  1250602
  Processing taxon: "OTU.154"
   taxon abs-abundance:  1244152
  Processing taxon: "OTU.3911"
   taxon abs-abundance:  1231438
  Processing taxon: "OTU.6978"
   taxon abs-abundance:  1224634
  Processing taxon: "OTU.139"
   taxon abs-abundance:  1219280
  Processing taxon: "OTU.5105"
   taxon abs-abundance:  1202037
  Processing taxon: "OTU.211"
   taxon abs-abundance:  1189837
  Processing taxon: "OTU.55"
   taxon abs-abundance:  1183706
  Processing taxon: "OTU.79"
   taxon abs-abundance:  1174248
  Processing taxon: "OTU.20"
   taxon abs-abundance:  8948635
  Processing taxon: "OTU.3745"
   taxon abs-abundance:  1171174
  Processing taxon: "OTU.5090"
   taxon abs-abundance:  1166669
  Processing taxon: "OTU.34"
   taxon abs-abundance:  1158468
  Processing taxon: "OTU.276"
   taxon abs-abundance:  1155310
  Processing taxon: "OTU.1082"
   taxon abs-abundance:  1144239
  Processing taxon: "OTU.57"
   taxon abs-abundance:  1141922
  Processing taxon: "OTU.95"
   taxon abs-abundance:  1141326
  Processing taxon: "OTU.45"
   taxon abs-abundance:  1140756
  Processing taxon: "OTU.44"
   taxon abs-abundance:  1138685
  Processing taxon: "OTU.22"
   taxon abs-abundance:  8647890
  Processing taxon: "OTU.11804"
   taxon abs-abundance:  1131321
  Processing taxon: "OTU.137"
   taxon abs-abundance:  1123155
  Processing taxon: "OTU.6069"
   taxon abs-abundance:  1114849
  Processing taxon: "OTU.117"
   taxon abs-abundance:  1112781
  Processing taxon: "OTU.408"
   taxon abs-abundance:  1092198
  Processing taxon: "OTU.288"
   taxon abs-abundance:  1084096
  Processing taxon: "OTU.219"
   taxon abs-abundance:  1082315
  Processing taxon: "OTU.234"
   taxon abs-abundance:  1071413
  Processing taxon: "OTU.13"
   taxon abs-abundance:  7386563
  Processing taxon: "OTU.290"
   taxon abs-abundance:  1069527
  Processing taxon: "OTU.4164"
   taxon abs-abundance:  1066078
  Processing taxon: "OTU.81"
   taxon abs-abundance:  6742163
  Processing taxon: "OTU.108"
   taxon abs-abundance:  6609322
  Processing taxon: "OTU.32"
   taxon abs-abundance:  6261332
  Processing taxon: "OTU.29"
   taxon abs-abundance:  6175404
  Processing taxon: "OTU.42"
   taxon abs-abundance:  6144346
  Processing taxon: "OTU.19"
   taxon abs-abundance:  5822590
  Processing taxon: "OTU.14"
   taxon abs-abundance:  5286308
  Processing taxon: "OTU.105"
   taxon abs-abundance:  5249532
  Processing taxon: "OTU.83"
   taxon abs-abundance:  5106462
  Processing taxon: "OTU.12"
   taxon abs-abundance:  4867450
  Processing taxon: "OTU.53"
   taxon abs-abundance:  4521994
  Processing taxon: "OTU.4"
   taxon abs-abundance:  4373707
  Processing taxon: "OTU.38"
   taxon abs-abundance:  4363471
  Processing taxon: "OTU.423"
   taxon abs-abundance:  4320221
  Processing taxon: "OTU.71"
   taxon abs-abundance:  4290476
  Processing taxon: "OTU.59"
   taxon abs-abundance:  4276202
  Processing taxon: "OTU.43"
   taxon abs-abundance:  4246448
  Processing taxon: "OTU.65"
   taxon abs-abundance:  4222978
  Processing taxon: "OTU.9"
   taxon abs-abundance:  4180938
  Processing taxon: "OTU.147"
   taxon abs-abundance:  4110210
  Processing taxon: "OTU.146"
   taxon abs-abundance:  4049218
  Processing taxon: "OTU.21"
   taxon abs-abundance:  3901072
  Processing taxon: "OTU.40"
   taxon abs-abundance:  3856945
  Processing taxon: "OTU.37"
   taxon abs-abundance:  3620376
  Processing taxon: "OTU.36"
   taxon abs-abundance:  3608355
  Processing taxon: "OTU.69"
   taxon abs-abundance:  3526280
  Processing taxon: "OTU.85"
   taxon abs-abundance:  3519220
  Processing taxon: "OTU.15"
   taxon abs-abundance:  3454675
  Processing taxon: "OTU.168"
   taxon abs-abundance:  3266107
  Processing taxon: "OTU.56"
   taxon abs-abundance:  3227954
  Processing taxon: "OTU.25"
   taxon abs-abundance:  3219464
  Processing taxon: "OTU.4318"
   taxon abs-abundance:  3206427
  Processing taxon: "OTU.6882"
   taxon abs-abundance:  3134584
  Processing taxon: "OTU.3608"
   taxon abs-abundance:  3128962
  Processing taxon: "OTU.6885"
   taxon abs-abundance:  3095090
  Processing taxon: "OTU.156"
   taxon abs-abundance:  3056117
  Processing taxon: "OTU.165"
   taxon abs-abundance:  3042385
  Processing taxon: "OTU.104"
   taxon abs-abundance:  2857245
  Processing taxon: "OTU.26"
   taxon abs-abundance:  2823178
  Processing taxon: "OTU.35"
   taxon abs-abundance:  2793515
  Processing taxon: "OTU.39"
   taxon abs-abundance:  2682756
  Processing taxon: "OTU.17"
   taxon abs-abundance:  2651206
  Processing taxon: "OTU.778"
   taxon abs-abundance:  2620666
  Processing taxon: "OTU.2176"
   taxon abs-abundance:  2614780
  Processing taxon: "OTU.23"
   taxon abs-abundance:  2590830
  Processing taxon: "OTU.164"
   taxon abs-abundance:  2582404
  Processing taxon: "OTU.100"
   taxon abs-abundance:  2578019
  Processing taxon: "OTU.30"
   taxon abs-abundance:  2575054
  Processing taxon: "OTU.176"
   taxon abs-abundance:  2527001
  Processing taxon: "OTU.63"
   taxon abs-abundance:  2522859
  Processing taxon: "OTU.4907"
   taxon abs-abundance:  2478888
  Processing taxon: "OTU.49"
   taxon abs-abundance:  2332884
  Processing taxon: "OTU.240"
   taxon abs-abundance:  2303649
  Processing taxon: "OTU.60"
   taxon abs-abundance:  2294808
  Processing taxon: "OTU.46"
   taxon abs-abundance:  2293790
  Processing taxon: "OTU.24"
   taxon abs-abundance:  2289871
  Processing taxon: "OTU.6439"
   taxon abs-abundance:  2287854
  Processing taxon: "OTU.2265"
   taxon abs-abundance:  2279768
  Processing taxon: "OTU.47"
   taxon abs-abundance:  2273489
  Processing taxon: "OTU.158"
   taxon abs-abundance:  2245100
  Processing taxon: "OTU.8395"
   taxon abs-abundance:  2221055
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1597"
   taxon abs-abundance:  2211464
  Processing taxon: "OTU.82"
   taxon abs-abundance:  2199492
  Processing taxon: "OTU.5092"
   taxon abs-abundance:  2192401
  Processing taxon: "OTU.52"
   taxon abs-abundance:  2175236
  Processing taxon: "OTU.175"
   taxon abs-abundance:  2134830
  Processing taxon: "OTU.50"
   taxon abs-abundance:  2130799
  Processing taxon: "OTU.92"
   taxon abs-abundance:  2036944
  Processing taxon: "OTU.6967"
   taxon abs-abundance:  1995117
  Processing taxon: "OTU.64"
   taxon abs-abundance:  1992529
  Processing taxon: "OTU.84"
   taxon abs-abundance:  1984579
  Processing taxon: "OTU.27"
   taxon abs-abundance:  1959526
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.695"
   taxon abs-abundance:  1957723
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.919"
   taxon abs-abundance:  1931009

Plotting taxon abundances


In [104]:
%%R -i workDir
setwd(workDir)

# loading file
tbl = read.delim('OTU_abs1e9.txt', sep='\t')

In [105]:
%%R
## BD for G+C of 0 or 100
BD.GCp0 = 0 * 0.098 + 1.66
BD.GCp100 = 1 * 0.098 + 1.66

In [106]:
%%R -w 800 -h 300
# plotting absolute abundances

tbl.s = tbl %>%
    group_by(library, BD_mid) %>%
    summarize(total_count = sum(count))

## plot
p = ggplot(tbl.s, aes(BD_mid, total_count)) +
    geom_area(stat='identity', alpha=0.3, position='dodge') +
    geom_histogram(stat='identity') +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16) 
    )
p



In [107]:
%%R -w 800 -h 300
# plotting number of taxa at each BD

tbl.nt = tbl %>%
    filter(count > 0) %>%
    group_by(library, BD_mid) %>%
    summarize(n_taxa = n())

## plot
p = ggplot(tbl.nt, aes(BD_mid, n_taxa)) +
    geom_area(stat='identity', alpha=0.3, position='dodge') +
    geom_histogram(stat='identity') +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density', y='Number of taxa') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p



In [108]:
%%R -w 800 -h 250
# plotting relative abundances

## plot
p = ggplot(tbl, aes(BD_mid, count, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity', position='dodge', alpha=0.5)



In [109]:
%%R -w 800 -h 250

p + geom_area(stat='identity', position='fill')


Subsampling from the OTU table


In [268]:
dist,loc,scale = seq_per_fraction

!cd $workDir; \
    SIPSim OTU_subsample \
    --dist $dist \
    --dist_params mean:$loc,sigma:$scale \
    --walk 2 \
    --min_size 10000 \
    --max_size 200000 \
    OTU_abs1e9.txt \
    > OTU_abs1e9_sub.txt

Testing/Plotting seq count distribution of subsampled fraction samples


In [269]:
%%R -h 300 -i workDir
setwd(workDir)

tbl = read.csv('OTU_abs1e9_sub.txt', sep='\t') 

tbl.s = tbl %>% 
    group_by(library, fraction) %>%
    summarize(total_count = sum(count)) %>%
    ungroup() %>%
    mutate(library = as.character(library))

ggplot(tbl.s, aes(total_count)) +
    geom_density(fill='blue')



In [270]:
%%R -h 300 -w 600
setwd(workDir)

tbl.s = tbl %>%
    group_by(fraction, BD_min, BD_mid, BD_max) %>%
    summarize(total_count = sum(count)) 

ggplot(tbl.s, aes(BD_mid, total_count)) +
    geom_point() +
    geom_line() +
    labs(x='Buoyant density', y='Total sequences') +
    theme_bw() +
    theme(
        text = element_text(size=16)
        )


Getting list of target taxa


In [271]:
%%R -i workDir

inFile = paste(c(workDir, 'target_genome_index.txt'), collapse='/')

tbl.target = read.delim(inFile, sep='\t', header=F)
colnames(tbl.target) = c('OTUId', 'genome_file', 'genome_ID', 'X', 'Y', 'Z')
tbl.target = tbl.target %>% distinct(OTUId)


cat('Number of target OTUs: ', tbl.target$OTUId %>% unique %>% length, '\n')
cat('----------\n')
tbl.target %>% head(n=3)


Number of target OTUs:  198 
----------
     OTUId
1 OTU.8540
2 OTU.9267
3 OTU.1457
                                                                                    genome_file
1 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
2 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
3 /home/nick/notebook/SIPSim/dev/bac_genome1210/genomes/Thermomonospora_curvata_DSM_43183.fasta
                                   genome_ID X           Y    Z
1 CP001738_Thermomonospora_curvata_DSM_43183 1 0.002582583 4561
2 CP001738_Thermomonospora_curvata_DSM_43183 1 0.005045402 2191
3 CP001738_Thermomonospora_curvata_DSM_43183 1 0.011258918 1106

Plotting abundance distributions


In [272]:
%%R -w 800 -h 250
# plotting relative abundances

tbl = tbl %>% 
    group_by(fraction) %>%
    mutate(rel_abund = count / sum(count))


## plot
p = ggplot(tbl, aes(BD_mid, count, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity', position='dodge', alpha=0.5)



In [273]:
%%R -w 800 -h 250

p = ggplot(tbl, aes(BD_mid, rel_abund, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity')


Abundance distribution of just target taxa


In [274]:
%%R

targets = tbl.target$OTUId %>% as.vector %>% unique 

tbl.f = tbl %>%
    filter(taxon %in% targets)

tbl.f %>% head


Source: local data frame [6 x 8]
Groups: fraction

  library    fraction taxon BD_min BD_mid BD_max count rel_abund
1       1  -inf-1.660 OTU.1   -Inf  1.659  1.659     0         0
2       1 1.660-1.665 OTU.1  1.660  1.663  1.665     0         0
3       1 1.665-1.668 OTU.1  1.665  1.667  1.668     0         0
4       1 1.668-1.670 OTU.1  1.668  1.669  1.670     0         0
5       1 1.670-1.672 OTU.1  1.670  1.671  1.672     0         0
6       1 1.672-1.675 OTU.1  1.672  1.673  1.675     0         0

In [275]:
%%R -w 800 -h 250
# plotting absolute abundances

## plot
p = ggplot(tbl.f, aes(BD_mid, count, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity', position='dodge', alpha=0.5)



In [276]:
%%R -w 800 -h 250
# plotting relative abundances

p = ggplot(tbl.f, aes(BD_mid, rel_abund, fill=taxon)) +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p + geom_area(stat='identity')


Plotting 'true' taxon abundance distribution (from priming exp dataset)


In [277]:
%%R -i metaDataFile
# loading priming_exp metadata file

meta = read.delim(metaDataFile, sep='\t')
meta %>% head(n=4)


            Sample FractionNum Bulk Control CC X100 X700 H2O Day Density rep
1 12C.000.28.03.07           7    0       1  1    0    0   0  28  1.7646    
2 12C.000.28.03.08           8    0       1  1    0    0   0  28  1.7614    
3 12C.000.28.03.09           9    0       1  1    0    0   0  28  1.7537    
4 12C.000.28.03.10          10    0       1  1    0    0   0  28  1.7483    
  contolVlabel Treatment
1      control    12C000
2      control    12C000
3      control    12C000
4      control    12C000

In [278]:
%%R -i otuTableFile
# loading priming_exp OTU table 

tbl.otu.true = read.delim(otuTableFile, sep='\t') %>%
    select(OTUId, starts_with('X12C.700.14')) 
tbl.otu.true %>% head(n=3)


     OTUId X12C.700.14.06.14 X12C.700.14.06.05 X12C.700.14.06.16
1 OTU.4776                34               142                11
2 OTU.2864                 1                16                 1
3 OTU.8170                 0                 0                 0
  X12C.700.14.06.11 X12C.700.14.06.13 X12C.700.14.06.09 X12C.700.14.06.04
1                18                30                27                97
2                 2                 0                 1                 3
3                 0                 0                 0                 0
  X12C.700.14.06.20 X12C.700.14.06.10 X12C.700.14.06.15 X12C.700.14.06.08
1               226                23                19                35
2                 1                 0                 1                 0
3                 0                 1                 0                 0
  X12C.700.14.06.12 X12C.700.14.06.18 X12C.700.14.06.17 X12C.700.14.06.19
1                25                61                27               136
2                 0                 2                 2                 0
3                 0                 0                 0                 0
  X12C.700.14.06.23 X12C.700.14.06.21 X12C.700.14.06.06 X12C.700.14.06.07
1                85               283                50                 0
2                 0                 1                 0                 0
3                 0                 0                 0                 0
  X12C.700.14.06.22 X12C.700.14.05.NA X12C.700.14.06.NA
1               208                51                26
2                 2                 0                 0
3                 0                 0                 0

In [279]:
%%R
# editing table
tbl.otu.true.w = tbl.otu.true %>%
    gather('sample', 'count', 2:ncol(tbl.otu.true)) %>%
    mutate(sample = gsub('^X', '', sample)) %>%
    group_by(sample) %>%
    mutate(rel_abund = count / sum(count)) %>%
    ungroup() %>%
    filter(count > 0)
tbl.otu.true.w %>% head(n=5)


Source: local data frame [5 x 4]

     OTUId           sample count    rel_abund
1 OTU.4776 12C.700.14.06.14    34 7.263716e-04
2 OTU.2864 12C.700.14.06.14     1 2.136387e-05
3 OTU.5406 12C.700.14.06.14     2 4.272774e-05
4 OTU.6001 12C.700.14.06.14     1 2.136387e-05
5  OTU.611 12C.700.14.06.14    23 4.913690e-04

In [280]:
%%R
tbl.true.j = inner_join(tbl.otu.true.w, meta, c('sample' = 'Sample'))
tbl.true.j %>% as.data.frame %>% head(n=3)


     OTUId           sample count    rel_abund FractionNum Bulk Control CC X100
1 OTU.4776 12C.700.14.06.14    34 7.263716e-04          14    0       1  0    0
2 OTU.2864 12C.700.14.06.14     1 2.136387e-05          14    0       1  0    0
3 OTU.5406 12C.700.14.06.14     2 4.272774e-05          14    0       1  0    0
  X700 H2O Day Density rep contolVlabel Treatment
1    1   0  14  1.7122          control    12C700
2    1   0  14  1.7122          control    12C700
3    1   0  14  1.7122          control    12C700

In [281]:
%%R -w 800 -h 300  -i workDir
# plotting number of taxa at each BD

tbl = read.csv('OTU_abs1e9_sub.txt', sep='\t') 

tbl.nt = tbl %>%
    filter(count > 0) %>%
    group_by(library, BD_mid) %>%
    summarize(n_taxa = n())

## plot
p = ggplot(tbl.nt, aes(BD_mid, n_taxa)) +
    geom_area(stat='identity', alpha=0.5) +
    geom_point() +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density', y='Number of taxa') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )
p



In [282]:
%%R -w 700 -h 350

tbl.true.j.s = tbl.true.j %>%
    filter(count > 0) %>%
    group_by(sample, Density) %>%
    summarize(n_taxa = sum(count > 0))

ggplot(tbl.true.j.s, aes(Density, n_taxa)) +
    geom_area(stat='identity', alpha=0.5) +
    geom_point() +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density', y='Number of taxa') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )


Plotting total counts for each sample


In [283]:
%%R -h 300 -w 600
tbl.true.j.s = tbl.true.j %>%
    group_by(sample, Density) %>%
    summarize(total_count = sum(count)) 

ggplot(tbl.true.j.s, aes(Density, total_count)) +
    geom_point() +
    geom_line() +
    labs(x='Buoyant density', y='Total sequences') +
    theme_bw() +
    theme(
        text = element_text(size=16)
        )


Plotting abundance distribution of target OTUs


In [284]:
%%R
tbl.true.j.f = tbl.true.j %>%
    filter(OTUId %in% targets) %>%
    arrange(OTUId, Density) %>%
    group_by(sample)
tbl.true.j.f %>% head(n=3) %>% as.data.frame


  OTUId           sample count  rel_abund FractionNum Bulk Control CC X100 X700
1 OTU.1 12C.700.14.06.23   736 0.02455871          23    0       1  0    0    1
2 OTU.1 12C.700.14.06.22  1229 0.02870556          22    0       1  0    0    1
3 OTU.1 12C.700.14.06.21  1560 0.03320067          21    0       1  0    0    1
  H2O Day Density rep contolVlabel Treatment
1   0  14  1.6772          control    12C700
2   0  14  1.6805          control    12C700
3   0  14  1.6849          control    12C700

In [285]:
%%R -w 800 -h 250
# plotting relative abundances

## plot
ggplot(tbl.true.j.f, aes(Density, rel_abund, fill=OTUId)) +
    geom_area(stat='identity') +
    geom_vline(xintercept=c(BD.GCp0, BD.GCp100), linetype='dashed', alpha=0.5) +
    labs(x='Buoyant density') +
    theme_bw() +
    theme( 
        text = element_text(size=16),
        legend.position = 'none'
    )


Combining true and simulated OTU tables for target taxa


In [289]:
%%R
tbl.f.e = tbl.f %>%
    mutate(library = 'simulation') %>%
    rename('density' = BD_mid) %>%
    select(-BD_min, -BD_max)

tbl.true.e = tbl.true.j.f %>% 
    select('taxon' = OTUId,
           'fraction' = sample,
           'density' = Density,
           count, rel_abund) %>%
    mutate(library = 'true') 
           
           
tbl.sim.true = rbind(tbl.f.e, tbl.true.e) %>% as.data.frame
tbl.f.e = data.frame()
tbl.true.e = data.frame()

tbl.sim.true %>% head(n=3)


     library    fraction taxon density count rel_abund
1 simulation  -inf-1.660 OTU.1   1.659     0         0
2 simulation 1.660-1.665 OTU.1   1.663     0         0
3 simulation 1.665-1.668 OTU.1   1.667     0         0

In [290]:
%%R
# check
cat('Number of target taxa: ', tbl.sim.true$taxon %>% unique %>% length, '\n')


Number of target taxa:  198 

Abundance distributions of each target taxon


In [291]:
%%R -w 900 -h 3500

tbl.sim.true.f = tbl.sim.true %>%
    ungroup() %>%
    filter(density >= 1.6772) %>%
    filter(density <= 1.7603) %>%
    group_by(taxon) %>%
    mutate(mean_rel_abund = mean(rel_abund))  %>%
    ungroup()

tbl.sim.true.f$taxon = reorder(tbl.sim.true.f$taxon, -tbl.sim.true.f$mean_rel_abund)

ggplot(tbl.sim.true.f, aes(density, rel_abund, color=library)) +
    geom_point() +
    geom_line() +
    theme_bw() +
    facet_wrap(~ taxon, ncol=4, scales='free_y')



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