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'
    • OTU Table
      • Total community abundance = 1e9
      • Adding PCR simulation step
      • Subsampling (sequencing simulation)
      • Adding count error drawn from a neg-binomial distribution

Setting variables


In [22]:
workDir = '/home/nick/notebook/SIPSim/dev/priming_exp/validation_sample/X12C.700.14_fracRichness-PCR-negBin/'
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 [23]:
import glob
import cPickle as pickle
import copy
from IPython.display import Image

In [24]:
%load_ext rpy2.ipython


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

In [25]:
%%R
library(ggplot2)
library(dplyr)
library(tidyr)
library(gridExtra)

## BD for G+C of 0 or 100
BD.GCp0 = 0 * 0.098 + 1.66
BD.GCp100 = 1 * 0.098 + 1.66

In [26]:
if not os.path.isdir(workDir):
    os.makedirs(workDir)

Creating a community file from the fraction relative abundances


In [27]:
%%R -i abundFile
# reading priming experiment OTU table
tbl.abund = read.delim(abundFile, sep='\t')
tbl.abund %>% head(n=4)


     OTUId mean_perc_abund median_perc_abund max_perc_abund      sample
1    OTU.1      3.82753232        3.92631730     5.60316872 X12C.700.14
2   OTU.10      0.04863100        0.04818209     0.08545617 X12C.700.14
3  OTU.100      0.30885091        0.31216647     0.50846009 X12C.700.14
4 OTU.1000      0.01354891        0.01388383     0.02444091 X12C.700.14

In [28]:
%%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(n=4)


  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

In [29]:
%%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(n=4)


Source: local data frame [4 x 4]

  library taxon_name rel_abund_perc  rank
    (chr)     (fctr)          (dbl) (int)
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

In [30]:
%%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 [32]:
%%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 [33]:
%%R -i workDir

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

In [34]:
%%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 [35]:
%%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 [36]:
%%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 [37]:
%%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 [38]:
%%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 [39]:
%%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 [40]:
%%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 [41]:
%%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 [42]:
!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 [46]:
%%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 [47]:
%%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 [48]:
%%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 [49]:
%%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 [50]:
# 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[50]:
['OTU.9280', 'OTU.8991', 'OTU.8467', 'OTU.7687']

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

In [54]:
# renaming randomly selected KDEs by non-target OTU-ID
for i in range(len(ampFrag_rand)):
    ampFrag_rand[i][0] = nonTarget[i]

In [55]:
# 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 [56]:
!cd $workDir; \
    SIPSim fragment_kde \
    ampFrags_wRand.pkl \
    > ampFrags_wRand_kde.pkl

Adding diffusion


In [57]:
!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.4684
Processing: OTU.4685
Processing: OTU.6773
Processing: OTU.757
Processing: OTU.2002
Processing: OTU.507
Processing: OTU.9232
Processing: OTU.5335
Processing: OTU.4683
Processing: OTU.1969
Processing: OTU.12933
Processing: OTU.2003
Processing: OTU.504
Processing: OTU.6231
Processing: OTU.6230
Processing: OTU.142
Processing: OTU.8214
Processing: OTU.1297
Processing: OTU.4680
Processing: OTU.12668
Processing: OTU.13575
Processing: OTU.6722
Processing: OTU.4929
Processing: OTU.505
Processing: OTU.6233
Processing: OTU.13948
Processing: OTU.5337
Processing: OTU.411
Processing: OTU.1294
Processing: OTU.4681
Processing: OTU.932
Processing: OTU.12666
Processing: OTU.13576
Processing: OTU.839
Processing: OTU.502
Processing: OTU.3604
Processing: OTU.6721
Processing: OTU.3425
Processing: OTU.13941
Processing: OTU.8216
Processing: OTU.1744
Processing: OTU.7608
Processing: OTU.4224
Processing: OTU.586
Processing: OTU.140
Processing: OTU.7874
Processing: OTU.1965
Processing: OTU.931
Processing: OTU.5555
Processing: OTU.2554
Processing: OTU.503
Processing: OTU.7048
Processing: OTU.6727
Processing: OTU.13942
Processing: OTU.3424
Processing: OTU.273
Processing: OTU.1745
Processing: OTU.9278
Processing: OTU.1305
Processing: OTU.6117
Processing: OTU.7816
Processing: OTU.7876
Processing: OTU.12664
Processing: OTU.930
Processing: OTU.4814
Processing: OTU.2007
Processing: OTU.5554
Processing: OTU.6335
Processing: OTU.500
Processing: OTU.7045
Processing: OTU.6726
Processing: OTU.3399
Processing: OTU.1776
Processing: OTU.13147
Processing: OTU.6959
Processing: OTU.5704
Processing: OTU.4226
Processing: OTU.274
Processing: OTU.7817
Processing: OTU.7815
Processing: OTU.3014
Processing: OTU.7872
Processing: OTU.1175
Processing: OTU.1960
Processing: OTU.937
Processing: OTU.2556
Processing: OTU.5557
Processing: OTU.6332
Processing: OTU.501
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Making an incorp config file


In [58]:
!cd $workDir; \
    SIPSim incorpConfigExample \
    --percTaxa 0 \
    --percIncorpUnif 100 \
    > PT0_PI100.config

Adding isotope incorporation to BD distribution


In [59]:
!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 [60]:
!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.8524
  Processing: OTU.1393
  Processing: OTU.4572
  Processing: OTU.3858
  Processing: OTU.216
  Processing: OTU.3897
  Processing: OTU.5023
  Processing: OTU.7218
  Processing: OTU.3038
  Processing: OTU.879
  Processing: OTU.2859
  Processing: OTU.1392
  Processing: OTU.1391
  Processing: OTU.4575
  Processing: OTU.3859
  Processing: OTU.6076
  Processing: OTU.3894
  Processing: OTU.7219
  Processing: OTU.5024
  Processing: OTU.3039
  Processing: OTU.2594
  Processing: OTU.2858
  Processing: OTU.1390
  Processing: OTU.46
  Processing: OTU.1689
  Processing: OTU.215
  Processing: OTU.3895
  Processing: OTU.2455
  Processing: OTU.6008
  Processing: OTU.5026
  Processing: OTU.2047
  Processing: OTU.10483
  Processing: OTU.2365
  Processing: OTU.1399
  Processing: OTU.4938
  Processing: OTU.1688
  Processing: OTU.13458
  Processing: OTU.2963
  Processing: OTU.2454
  Processing: OTU.5987
  Processing: OTU.5029
  Processing: OTU.2596
  Processing: OTU.4803
  Processing: OTU.1398
  Processing: OTU.6112
  Processing: OTU.1056
  Processing: OTU.12754
  Processing: OTU.210
  Processing: OTU.2887
  Processing: OTU.7236
  Processing: OTU.5028
  Processing: OTU.2045
  Processing: OTU.11420
  Processing: OTU.3739
  Processing: OTU.45
  Processing: OTU.1681
  Processing: OTU.10172
  Processing: OTU.13378
  Processing: OTU.7237
  Processing: OTU.4883
  Processing: OTU.601
  Processing: OTU.2590
  Processing: OTU.11424
  Processing: OTU.3738
  Processing: OTU.280
  Processing: OTU.1680
  Processing: OTU.8509
  Processing: OTU.7233
  Processing: OTU.4884
  Processing: OTU.12993
  Processing: OTU.2361
  Processing: OTU.2591
  Processing: OTU.1585
  Processing: OTU.3735
  Processing: OTU.1683
  Processing: OTU.8508
  Processing: OTU.7230
  Processing: OTU.4885
  Processing: OTU.12995
  Processing: OTU.400
  Processing: OTU.2040
  Processing: OTU.2593
  Processing: OTU.43
  Processing: OTU.1682
  Processing: OTU.6073
  Processing: OTU.7238
  Processing: OTU.2453
  Processing: OTU.5128
  Processing: OTU.406
  Processing: OTU.2598
  Processing: OTU.6648
  Processing: OTU.1685
  Processing: OTU.5821
  Processing: OTU.7239
  Processing: OTU.2459
  Processing: OTU.5129
  Processing: OTU.14266
  Processing: OTU.2599
  Processing: OTU.9164
  Processing: OTU.1684
  Processing: OTU.5820
  Processing: OTU.8468
  Processing: OTU.2458
  Processing: OTU.5125
  Processing: OTU.8747
  Processing: OTU.2048
  Processing: OTU.285
  Processing: OTU.1686
  Processing: OTU.5823
  Processing: OTU.1906
  Processing: OTU.5127
  Processing: OTU.8740
  Processing: OTU.663
  Processing: OTU.2112
  Processing: OTU.5575
  Processing: OTU.8502
  Processing: OTU.1907
  Processing: OTU.5121
  Processing: OTU.405
  Processing: OTU.5866
  Processing: OTU.6642
  Processing: OTU.7788
  Processing: OTU.5825
  Processing: OTU.1904
  Processing: OTU.5123
  Processing: OTU.662
  Processing: OTU.8749
  Processing: OTU.284
  Processing: OTU.3269
  Processing: OTU.5827
  Processing: OTU.1905
  Processing: OTU.6132
  Processing: OTU.705
  Processing: OTU.404
  Processing: OTU.403
  Processing: OTU.5721
  Processing: OTU.3268
  Processing: OTU.5826
  Processing: OTU.1902
  Processing: OTU.602
  Processing: OTU.2628
  Processing: OTU.3078
  Processing: OTU.14356
  Processing: OTU.2039
  Processing: OTU.2837
  Processing: OTU.5552
  Processing: OTU.1903
  Processing: OTU.2629
  Processing: OTU.3261
  Processing: OTU.3260
  Processing: OTU.538
  Processing: OTU.3079
  Processing: OTU.2836
  Processing: OTU.8192
  Processing: OTU.1900
  Processing: OTU.700
  Processing: OTU.3264
  Processing: OTU.5727
  Processing: OTU.3071
  Processing: OTU.8193
  Processing: OTU.8194
  Processing: OTU.2834
  Processing: OTU.1908
  Processing: OTU.701
  Processing: OTU.3267
  Processing: OTU.4930
  Processing: OTU.3072
  Processing: OTU.8199
  Processing: OTU.2833
  Processing: OTU.1909
  Processing: OTU.702
  Processing: OTU.3266
  Processing: OTU.5724
  Processing: OTU.3075
  Processing: OTU.6130
  Processing: OTU.2832
  Processing: OTU.1920
  Processing: OTU.703
  Processing: OTU.810
  Processing: OTU.536
  Processing: OTU.3076
  Processing: OTU.8991
  Processing: OTU.2831
  Processing: OTU.4557
  Processing: OTU.2622
  Processing: OTU.811
  Processing: OTU.4932
  Processing: OTU.401
  Processing: OTU.8996
  Processing: OTU.2830
  Processing: OTU.4658
  Processing: OTU.2623
  Processing: OTU.812
  Processing: OTU.4933
  Processing: OTU.469
  Processing: OTU.8997
  Processing: OTU.10355
  Processing: OTU.5591
  Processing: OTU.2620
  Processing: OTU.813
  Processing: OTU.4934
  Processing: OTU.468
  Processing: OTU.7748
  Processing: OTU.1130
  Processing: OTU.5590
  Processing: OTU.5593
  Processing: OTU.2621
  Processing: OTU.814
  Processing: OTU.4935
  Processing: OTU.2479
  Processing: OTU.7749
  Processing: OTU.2839
  Processing: OTU.5597
  Processing: OTU.708
  Processing: OTU.815
  Processing: OTU.2031
  Processing: OTU.2477
  Processing: OTU.464
  Processing: OTU.7741
  Processing: OTU.1734
  Processing: OTU.5596
  Processing: OTU.2627
  Processing: OTU.816
  Processing: OTU.1057
  Processing: OTU.7746
  Processing: OTU.2624
  Processing: OTU.2625
  Processing: OTU.4247
  Processing: OTU.5598
  Processing: OTU.817
  Processing: OTU.530
  Processing: OTU.7745
  Processing: OTU.661
  Processing: OTU.4244
  Processing: OTU.12603
  Processing: OTU.818
  Processing: OTU.2025
  Processing: OTU.3527
  Processing: OTU.4298
  Processing: OTU.12291
  Processing: OTU.12604
  Processing: OTU.4653
  Processing: OTU.2027
  Processing: OTU.3524
  Processing: OTU.4294
  Processing: OTU.12290
  Processing: OTU.8820
  Processing: OTU.4245
  Processing: OTU.2020
  Processing: OTU.3037
  Processing: OTU.14148
  Processing: OTU.4296
  Processing: OTU.13808
  Processing: OTU.13806
  Processing: OTU.12296
  Processing: OTU.1362
  Processing: OTU.2022
  Processing: OTU.3522
  Processing: OTU.4291
  Processing: OTU.12295
  Processing: OTU.13801
  Processing: OTU.1137
  Processing: OTU.2023
  Processing: OTU.14140
  Processing: OTU.4290
  Processing: OTU.12299
  Processing: OTU.5047
  Processing: OTU.6071
  Processing: OTU.5572
  Processing: OTU.14142
  Processing: OTU.6123
  Processing: OTU.5046
  Processing: OTU.1363
  Processing: OTU.3198
  Processing: OTU.3194
  Processing: OTU.9789
  Processing: OTU.660
  Processing: OTU.5045
  Processing: OTU.3192
  Processing: OTU.1187
  Processing: OTU.11643
  Processing: OTU.692
  Processing: OTU.3191
  Processing: OTU.5044
  Processing: OTU.11642
  Processing: OTU.693
  Processing: OTU.3190
  Processing: OTU.5042
  Processing: OTU.3032
  Processing: OTU.922
  Processing: OTU.5691
  Processing: OTU.5041
  Processing: OTU.9782
  Processing: OTU.3033
  Processing: OTU.9785
  Processing: OTU.4429
  Processing: OTU.2819
  Processing: OTU.2818

In [61]:
%%R -i workDir
# plotting BD-shift counts

setwd(workDir)
df = read.delim('ampFrags_wRand_kde_dif_incorp_BD-shift.txt', sep='\t')

ggplot(df, aes(BD_shift)) +
    geom_histogram()


/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to adjust this.

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

Simulating gradient fractions


In [62]:
!cd $workDir; \
    SIPSim gradient_fractions \
    comm.txt \
    > fracs.txt

Simulating an OTU table


In [63]:
!cd $workDir; \
    SIPSim OTU_table \
    ampFrags_wRand_kde_dif_incorp.pkl \
    comm.txt \
    fracs.txt \
    --abs 5e9 \
    --np $nprocs \
    > OTU_abs5e9.txt


Loading files...
Simulating OTUs...
Processing library: "1"
  Processing taxon: "OTU.1"
   taxon abs-abundance:  159744554
  Processing taxon: "OTU.159"
   taxon abs-abundance:  9618842
  Processing taxon: "OTU.129"
   taxon abs-abundance:  5324969
  Processing taxon: "OTU.98"
   taxon abs-abundance:  3700347
  Processing taxon: "OTU.270"
   taxon abs-abundance:  2730413
  Processing taxon: "OTU.177"
   taxon abs-abundance:  2117272
  Processing taxon: "OTU.5917"
   taxon abs-abundance:  1670863
  Processing taxon: "OTU.3332"
   taxon abs-abundance:  1395964
  Processing taxon: "OTU.2144"
   taxon abs-abundance:  1142654
  Processing taxon: "OTU.8004"
  Processing taxon: "OTU.6767"
   taxon abs-abundance:  2727189
   taxon abs-abundance:  2113842
  Processing taxon: "OTU.669"
   taxon abs-abundance:  985465
  Processing taxon: "OTU.1128"
   taxon abs-abundance:  1667363
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1814"
   taxon abs-abundance:  1664467
  Processing taxon: "OTU.5914"
   taxon abs-abundance:  3698094
  Processing taxon: "OTU.3477"
   taxon abs-abundance:  1389694
  Processing taxon: "OTU.504"
   taxon abs-abundance:  853246
  Processing taxon: "OTU.8003"
   taxon abs-abundance:  1142372
  Processing taxon: "OTU.2372"
   taxon abs-abundance:  984295
  Processing taxon: "OTU.414"
   taxon abs-abundance:  758479
  Processing taxon: "OTU.1528"
   taxon abs-abundance:  5287360
  Processing taxon: "OTU.732"
   taxon abs-abundance:  852840
  Processing taxon: "OTU.1127"
   taxon abs-abundance:  661193
  Processing taxon: "OTU.878"
   taxon abs-abundance:  1384606
  Processing taxon: "OTU.373"
   taxon abs-abundance:  1136792
  Processing taxon: "OTU.616"
  Processing taxon: "OTU.8941"
   taxon abs-abundance:  1659845
   taxon abs-abundance:  758457
  Processing taxon: "OTU.709"
   taxon abs-abundance:  984156
  Processing taxon: "OTU.1010"
   taxon abs-abundance:  2112092
  Processing taxon: "OTU.509"
   taxon abs-abundance:  852335
  Processing taxon: "OTU.4715"
   taxon abs-abundance:  581623
  Processing taxon: "OTU.794"
   taxon abs-abundance:  660328
  Processing taxon: "OTU.7834"
   taxon abs-abundance:  756427
  Processing taxon: "OTU.386"
   taxon abs-abundance:  2722339
  Processing taxon: "OTU.1702"
   taxon abs-abundance:  580747
  Processing taxon: "OTU.2530"
   taxon abs-abundance:  1133952
  Processing taxon: "OTU.192"
   taxon abs-abundance:  981022
  Processing taxon: "OTU.8712"
   taxon abs-abundance:  526384
  Processing taxon: "OTU.900"
   taxon abs-abundance:  660161
  Processing taxon: "OTU.2923"
   taxon abs-abundance:  851655
  Processing taxon: "OTU.8842"
   taxon abs-abundance:  1384086
  Processing taxon: "OTU.985"
   taxon abs-abundance:  756351
  Processing taxon: "OTU.5904"
   taxon abs-abundance:  580370
  Processing taxon: "OTU.323"
   taxon abs-abundance:  1658233
  Processing taxon: "OTU.2633"
  Processing taxon: "OTU.658"
   taxon abs-abundance:  659400
   taxon abs-abundance:  475309
  Processing taxon: "OTU.383"
   taxon abs-abundance:  977072
  Processing taxon: "OTU.6102"
   taxon abs-abundance:  850940
  Processing taxon: "OTU.289"
   taxon abs-abundance:  3695020
  Processing taxon: "OTU.2771"
  Processing taxon: "OTU.13701"
  Processing taxon: "OTU.2414"
   taxon abs-abundance:  1130431
   taxon abs-abundance:  526292
   taxon abs-abundance:  580360
  Processing taxon: "OTU.758"
   taxon abs-abundance:  755140
  Processing taxon: "OTU.369"
   taxon abs-abundance:  2106566
  Processing taxon: "OTU.2347"
   taxon abs-abundance:  658615
  Processing taxon: "OTU.368"
   taxon abs-abundance:  434891
  Processing taxon: "OTU.542"
   taxon abs-abundance:  1379774
  Processing taxon: "OTU.6134"
   taxon abs-abundance:  579451
  Processing taxon: "OTU.1136"
   taxon abs-abundance:  475229
  Processing taxon: "OTU.984"
   taxon abs-abundance:  850770
  Processing taxon: "OTU.13643"
   taxon abs-abundance:  754894
  Processing taxon: "OTU.1565"
   taxon abs-abundance:  434413
  Processing taxon: "OTU.530"
   taxon abs-abundance:  975242
  Processing taxon: "OTU.12515"
   taxon abs-abundance:  525200
  Processing taxon: "OTU.12448"
   taxon abs-abundance:  658013
  Processing taxon: "OTU.140"
   taxon abs-abundance:  1128252
  Processing taxon: "OTU.233"
   taxon abs-abundance:  1657397
  Processing taxon: "OTU.4656"
   taxon abs-abundance:  407552
  Processing taxon: "OTU.101"
   taxon abs-abundance:  9491433
  Processing taxon: "OTU.1270"
   taxon abs-abundance:  579307
  Processing taxon: "OTU.4707"
   taxon abs-abundance:  2722096
  Processing taxon: "OTU.5541"
   taxon abs-abundance:  433899
  Processing taxon: "OTU.664"
   taxon abs-abundance:  754887
  Processing taxon: "OTU.841"
   taxon abs-abundance:  850501
  Processing taxon: "OTU.6906"
   taxon abs-abundance:  475108
  Processing taxon: "OTU.648"
   taxon abs-abundance:  657503
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.8572"
   taxon abs-abundance:  652784
  Processing taxon: "OTU.795"
   taxon abs-abundance:  433787
  Processing taxon: "OTU.1638"
   taxon abs-abundance:  1376917
  Processing taxon: "OTU.12077"
   taxon abs-abundance:  375137
  Processing taxon: "OTU.753"
   taxon abs-abundance:  406932
  Processing taxon: "OTU.4617"
   taxon abs-abundance:  524609
  Processing taxon: "OTU.550"
   taxon abs-abundance:  2103113
  Processing taxon: "OTU.2351"
   taxon abs-abundance:  433663
  Processing taxon: "OTU.398"
   taxon abs-abundance:  1128017
  Processing taxon: "OTU.473"
   taxon abs-abundance:  975186
  Processing taxon: "OTU.298"
   taxon abs-abundance:  651254
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.515"
   taxon abs-abundance:  651063
  Processing taxon: "OTU.416"
   taxon abs-abundance:  578429
  Processing taxon: "OTU.7337"
   taxon abs-abundance:  848618
  Processing taxon: "OTU.853"
   taxon abs-abundance:  753774
  Processing taxon: "OTU.412"
   taxon abs-abundance:  473685
  Processing taxon: "OTU.2183"
   taxon abs-abundance:  352836
  Processing taxon: "OTU.2606"
   taxon abs-abundance:  433271
  Processing taxon: "OTU.3330"
   taxon abs-abundance:  374772
  Processing taxon: "OTU.103"
   taxon abs-abundance:  1656049
  Processing taxon: "OTU.3459"
   taxon abs-abundance:  406469
  Processing taxon: "OTU.8534"
   taxon abs-abundance:  650291
  Processing taxon: "OTU.563"
   taxon abs-abundance:  433239
  Processing taxon: "OTU.2298"
   taxon abs-abundance:  521946
  Processing taxon: "OTU.874"
   taxon abs-abundance:  753098
  Processing taxon: "OTU.284"
   taxon abs-abundance:  848304
  Processing taxon: "OTU.410"
  Processing taxon: "OTU.4996"
   taxon abs-abundance:  352547
   taxon abs-abundance:  1127508
  Processing taxon: "OTU.949"
   taxon abs-abundance:  374742
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.2364"
   taxon abs-abundance:  374673
  Processing taxon: "OTU.873"
   taxon abs-abundance:  433118
  Processing taxon: "OTU.1034"
   taxon abs-abundance:  974599
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.3841"
   taxon abs-abundance:  973680
  Processing taxon: "OTU.350"
  Processing taxon: "OTU.954"
   taxon abs-abundance:  578223
   taxon abs-abundance:  472009
  Processing taxon: "OTU.440"
   taxon abs-abundance:  406308
  Processing taxon: "OTU.344"
   taxon abs-abundance:  647259
  Processing taxon: "OTU.172"
   taxon abs-abundance:  3686616
  Processing taxon: "OTU.4450"
   taxon abs-abundance:  1375266
  Processing taxon: "OTU.1283"
   taxon abs-abundance:  433112
  Processing taxon: "OTU.756"
   taxon abs-abundance:  749871
  Processing taxon: "OTU.1187"
  Processing taxon: "OTU.6450"
   taxon abs-abundance:  352514
   taxon abs-abundance:  2706280
  Processing taxon: "OTU.1689"
  Processing taxon: "OTU.7306"
   taxon abs-abundance:  847956
   taxon abs-abundance:  521946
  Processing taxon: "OTU.1277"
   taxon abs-abundance:  374450
  Processing taxon: "OTU.3358"
   taxon abs-abundance:  2101769
  Processing taxon: "OTU.4943"
   taxon abs-abundance:  645874
  Processing taxon: "OTU.2626"
   taxon abs-abundance:  433030
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.950"
   taxon abs-abundance:  432474
  Processing taxon: "OTU.893"
   taxon abs-abundance:  406128
  Processing taxon: "OTU.870"
   taxon abs-abundance:  1123681
  Processing taxon: "OTU.419"
   taxon abs-abundance:  1650377
  Processing taxon: "OTU.231"
   taxon abs-abundance:  973078
  Processing taxon: "OTU.594"
   taxon abs-abundance:  471204
  Processing taxon: "OTU.973"
   taxon abs-abundance:  576760
  Processing taxon: "OTU.8756"
   taxon abs-abundance:  352377
  Processing taxon: "OTU.1489"
   taxon abs-abundance:  746986
  Processing taxon: "OTU.1376"
   taxon abs-abundance:  431810
  Processing taxon: "OTU.482"
   taxon abs-abundance:  374346
  Processing taxon: "OTU.12647"
   taxon abs-abundance:  845613
  Processing taxon: "OTU.687"
   taxon abs-abundance:  645773
  Processing taxon: "OTU.8126"
   taxon abs-abundance:  521946
  Processing taxon: "OTU.5830"
   taxon abs-abundance:  405431
  Processing taxon: "OTU.2708"
   taxon abs-abundance:  431492
  Processing taxon: "OTU.854"
   taxon abs-abundance:  352009
  Processing taxon: "OTU.717"
  Processing taxon: "OTU.1415"
   taxon abs-abundance:  970432
   taxon abs-abundance:  470613
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.2388"
   taxon abs-abundance:  470387
  Processing taxon: "OTU.774"
   taxon abs-abundance:  745125
  Processing taxon: "OTU.3062"
   taxon abs-abundance:  1122238
  Processing taxon: "OTU.6073"
  Processing taxon: "OTU.601"
   taxon abs-abundance:  645080
   taxon abs-abundance:  374116
  Processing taxon: "OTU.1692"
   taxon abs-abundance:  431367
  Processing taxon: "OTU.3817"
   taxon abs-abundance:  845230
  Processing taxon: "OTU.426"
   taxon abs-abundance:  574917
  Processing taxon: "OTU.7572"
   taxon abs-abundance:  405282
  Processing taxon: "OTU.748"
   taxon abs-abundance:  1643354
  Processing taxon: "OTU.10055"
   taxon abs-abundance:  351948
  Processing taxon: "OTU.746"
   taxon abs-abundance:  431301
  Processing taxon: "OTU.897"
   taxon abs-abundance:  520253
  Processing taxon: "OTU.254"
   taxon abs-abundance:  744427
  Processing taxon: "OTU.1558"
   taxon abs-abundance:  644462
  Processing taxon: "OTU.190"
   taxon abs-abundance:  2090794
  Processing taxon: "OTU.1734"
  Processing taxon: "OTU.449"
   taxon abs-abundance:  374072
  Processing taxon: "OTU.4070"
   taxon abs-abundance:  970164
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1292"
   taxon abs-abundance:  969356
   taxon abs-abundance:  470042
  Processing taxon: "OTU.1412"
   taxon abs-abundance:  1374443
  Processing taxon: "OTU.10985"
   taxon abs-abundance:  431107
  Processing taxon: "OTU.3886"
   taxon abs-abundance:  840988
   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:  299998
   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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