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'
    • Adding PCR simulation step

Setting variables


In [32]:
workDir = '/home/nick/notebook/SIPSim/dev/priming_exp/validation_sample/X12C.700.14_fracRichness-PCR/'
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 [4]:
import glob
import cPickle as pickle
import copy
from IPython.display import Image

In [5]:
%load_ext rpy2.ipython

In [33]:
%%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 [7]:
if not os.path.isdir(workDir):
    os.makedirs(workDir)

Creating a community file from the fraction relative abundances


In [6]:
%%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 [7]:
%%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 [8]:
%%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 [9]:
%%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 [10]:
%%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 [11]:
%%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 [12]:
%%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 [13]:
%%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 [14]:
%%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 [15]:
%%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 [16]:
%%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 [17]:
%%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 [18]:
%%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 [19]:
%%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 [20]:
!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 [21]:
%%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 [22]:
%%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 [23]:
%%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 [24]:
%%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 [25]:
# 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[25]:
['OTU.9280', 'OTU.8991', 'OTU.8467', 'OTU.7687']

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

In [29]:
# renaming randomly selected KDEs by non-target OTU-ID
for i in range(len(ampFrag_rand)):
    ampFrag_rand[i][0] = nonTarget[i]

In [30]:
# 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 [31]:
!cd $workDir; \
    SIPSim fragment_kde \
    ampFrags_wRand.pkl \
    > ampFrags_wRand_kde.pkl

Adding diffusion


In [32]:
!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.6773
Processing: OTU.4687
Processing: OTU.2002
Processing: OTU.507
Processing: OTU.9232
Processing: OTU.5335
Processing: OTU.757
Processing: OTU.4684
Processing: OTU.12933
Processing: OTU.2003
Processing: OTU.504
Processing: OTU.6236
Processing: OTU.142
Processing: OTU.8214
Processing: OTU.1294
Processing: OTU.1969
Processing: OTU.4685
Processing: OTU.13575
Processing: OTU.4929
Processing: OTU.4398
Processing: OTU.505
Processing: OTU.6231
Processing: OTU.4928
Processing: OTU.411
Processing: OTU.5337
Processing: OTU.7608
Processing: OTU.12668
Processing: OTU.4683
Processing: OTU.2807
Processing: OTU.13576
Processing: OTU.839
Processing: OTU.6722
Processing: OTU.502
Processing: OTU.6147
Processing: OTU.6230
Processing: OTU.412
Processing: OTU.13948
Processing: OTU.1308
Processing: OTU.8216
Processing: OTU.9278
Processing: OTU.12666
Processing: OTU.4680
Processing: OTU.5555
Processing: OTU.933
Processing: OTU.7874
Processing: OTU.2006
Processing: OTU.6721
Processing: OTU.503
Processing: OTU.273
Processing: OTU.6146
Processing: OTU.3425
Processing: OTU.6233
Processing: OTU.4814
Processing: OTU.13941
Processing: OTU.4229
Processing: OTU.4996
Processing: OTU.3014
Processing: OTU.6959
Processing: OTU.4681
Processing: OTU.5554
Processing: OTU.932
Processing: OTU.7876
Processing: OTU.1965
Processing: OTU.6335
Processing: OTU.2007
Processing: OTU.6727
Processing: OTU.500
Processing: OTU.274
Processing: OTU.3424
Processing: OTU.3604
Processing: OTU.1776
Processing: OTU.7642
Processing: OTU.13942
Processing: OTU.4224
Processing: OTU.1745
Processing: OTU.13147
Processing: OTU.3155
Processing: OTU.11627
Processing: OTU.1176
Processing: OTU.7816
Processing: OTU.5557
Processing: OTU.931
Processing: OTU.7872
Processing: OTU.6332
Processing: OTU.2556
Processing: OTU.9046
Processing: OTU.501
Processing: OTU.12664
Processing: OTU.3399
Processing: OTU.7048
Processing: OTU.1771
Processing: OTU.275
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Making an incorp config file


In [33]:
!cd $workDir; \
    SIPSim incorpConfigExample \
    --percTaxa 0 \
    --percIncorpUnif 100 \
    > PT0_PI100.config

Adding isotope incorporation to BD distribution


In [34]:
!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 [35]:
!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.11905
  Processing: OTU.3038
  Processing: OTU.5825
  Processing: OTU.3285
  Processing: OTU.5866
  Processing: OTU.117
  Processing: OTU.2453
  Processing: OTU.5724
  Processing: OTU.288
  Processing: OTU.12993
  Processing: OTU.405
  Processing: OTU.1397
  Processing: OTU.1395
  Processing: OTU.5575
  Processing: OTU.8539
  Processing: OTU.525
  Processing: OTU.3284
  Processing: OTU.5827
  Processing: OTU.3039
  Processing: OTU.662
  Processing: OTU.440
  Processing: OTU.2459
  Processing: OTU.4932
  Processing: OTU.8749
  Processing: OTU.1394
  Processing: OTU.7788
  Processing: OTU.12995
  Processing: OTU.1572
  Processing: OTU.3283
  Processing: OTU.466
  Processing: OTU.705
  Processing: OTU.5826
  Processing: OTU.447
  Processing: OTU.6008
  Processing: OTU.2458
  Processing: OTU.4933
  Processing: OTU.404
  Processing: OTU.1393
  Processing: OTU.3269
  Processing: OTU.5128
  Processing: OTU.4091
  Processing: OTU.3282
  Processing: OTU.2628
  Processing: OTU.446
  Processing: OTU.2837
  Processing: OTU.526
  Processing: OTU.5987
  Processing: OTU.1906
  Processing: OTU.403
  Processing: OTU.2033
  Processing: OTU.1392
  Processing: OTU.3268
  Processing: OTU.5129
  Processing: OTU.3281
  Processing: OTU.2629
  Processing: OTU.113
  Processing: OTU.2836
  Processing: OTU.4541
  Processing: OTU.12677
  Processing: OTU.7236
  Processing: OTU.7237
  Processing: OTU.3078
  Processing: OTU.1391
  Processing: OTU.1907
  Processing: OTU.293
  Processing: OTU.3261
  Processing: OTU.700
  Processing: OTU.444
  Processing: OTU.7443
  Processing: OTU.5125
  Processing: OTU.2834
  Processing: OTU.4540
  Processing: OTU.4543
  Processing: OTU.1007
  Processing: OTU.7233
  Processing: OTU.3079
  Processing: OTU.1390
  Processing: OTU.3260
  Processing: OTU.1904
  Processing: OTU.4935
  Processing: OTU.701
  Processing: OTU.7442
  Processing: OTU.2411
  Processing: OTU.2833
  Processing: OTU.5127
  Processing: OTU.1570
  Processing: OTU.1006
  Processing: OTU.7230
  Processing: OTU.3071
  Processing: OTU.1399
  Processing: OTU.3264
  Processing: OTU.1905
  Processing: OTU.2031
  Processing: OTU.702
  Processing: OTU.7444
  Processing: OTU.2410
  Processing: OTU.2832
  Processing: OTU.5121
  Processing: OTU.4545
  Processing: OTU.3898
  Processing: OTU.7238
  Processing: OTU.1398
  Processing: OTU.3072
  Processing: OTU.3267
  Processing: OTU.703
  Processing: OTU.1902
  Processing: OTU.1057
  Processing: OTU.2413
  Processing: OTU.7447
  Processing: OTU.2831
  Processing: OTU.5123
  Processing: OTU.4544
  Processing: OTU.3899
  Processing: OTU.3739
  Processing: OTU.3075
  Processing: OTU.7239
  Processing: OTU.3266
  Processing: OTU.2622
  Processing: OTU.2412
  Processing: OTU.3288
  Processing: OTU.1903
  Processing: OTU.530
  Processing: OTU.2830
  Processing: OTU.602
  Processing: OTU.3738
  Processing: OTU.1067
  Processing: OTU.3076
  Processing: OTU.1003
  Processing: OTU.8468
  Processing: OTU.2623
  Processing: OTU.810
  Processing: OTU.2415
  Processing: OTU.300
  Processing: OTU.1900
  Processing: OTU.3527
  Processing: OTU.10355
  Processing: OTU.3735
  Processing: OTU.5552
  Processing: OTU.401
  Processing: OTU.1066
  Processing: OTU.1002
  Processing: OTU.2620
  Processing: OTU.811
  Processing: OTU.2414
  Processing: OTU.301
  Processing: OTU.1908
  Processing: OTU.1130
  Processing: OTU.3524
  Processing: OTU.3734
  Processing: OTU.469
  Processing: OTU.8192
  Processing: OTU.4549
  Processing: OTU.1001
  Processing: OTU.2621
  Processing: OTU.812
  Processing: OTU.2417
  Processing: OTU.302
  Processing: OTU.2839
  Processing: OTU.1909
  Processing: OTU.3037
  Processing: OTU.3733
  Processing: OTU.468
  Processing: OTU.8193
  Processing: OTU.708
  Processing: OTU.4548
  Processing: OTU.813
  Processing: OTU.1000
  Processing: OTU.2416
  Processing: OTU.4247
  Processing: OTU.4244
  Processing: OTU.1920
  Processing: OTU.14148
  Processing: OTU.3522
  Processing: OTU.2479
  Processing: OTU.2477
  Processing: OTU.8194
  Processing: OTU.2627
  Processing: OTU.814
  Processing: OTU.3892
  Processing: OTU.4096
  Processing: OTU.4557
  Processing: OTU.14140
  Processing: OTU.4653
  Processing: OTU.464
  Processing: OTU.2624
  Processing: OTU.8199
  Processing: OTU.815
  Processing: OTU.3893
  Processing: OTU.4095
  Processing: OTU.14142
  Processing: OTU.467
  Processing: OTU.4658
  Processing: OTU.4245
  Processing: OTU.2625
  Processing: OTU.816
  Processing: OTU.6130
  Processing: OTU.3890
  Processing: OTU.13433
  Processing: OTU.9789
  Processing: OTU.2474
  Processing: OTU.1362
  Processing: OTU.5591
  Processing: OTU.661
  Processing: OTU.817
  Processing: OTU.8991
  Processing: OTU.3891
  Processing: OTU.3896
  Processing: OTU.13434
  Processing: OTU.11643
  Processing: OTU.1137
  Processing: OTU.12291
  Processing: OTU.5590
  Processing: OTU.818
  Processing: OTU.8996
  Processing: OTU.3897
  Processing: OTU.13436
  Processing: OTU.11642
  Processing: OTU.6071
  Processing: OTU.5593
  Processing: OTU.12290
  Processing: OTU.819
  Processing: OTU.8997
  Processing: OTU.7748
  Processing: OTU.3894
  Processing: OTU.7939
  Processing: OTU.3032
  Processing: OTU.1363
  Processing: OTU.12296
  Processing: OTU.2027
  Processing: OTU.5597
  Processing: OTU.7749
  Processing: OTU.7741
  Processing: OTU.3895
  Processing: OTU.9782
  Processing: OTU.7938
  Processing: OTU.3978
  Processing: OTU.12295
  Processing: OTU.2020
  Processing: OTU.5596
  Processing: OTU.7746
  Processing: OTU.13458
  Processing: OTU.6001
  Processing: OTU.7931
  Processing: OTU.8764
  Processing: OTU.2022
  Processing: OTU.5598
  Processing: OTU.12299
  Processing: OTU.7745
  Processing: OTU.13104
  Processing: OTU.9785
  Processing: OTU.7933
  Processing: OTU.2023
  Processing: OTU.4241
  Processing: OTU.6123
  Processing: OTU.12603
  Processing: OTU.4298
  Processing: OTU.4429
  Processing: OTU.5572
  Processing: OTU.660
  Processing: OTU.12604
  Processing: OTU.4294
  Processing: OTU.2819
  Processing: OTU.3198
  Processing: OTU.8820
  Processing: OTU.692
  Processing: OTU.4296
  Processing: OTU.2818
  Processing: OTU.3194
  Processing: OTU.13808
  Processing: OTU.921
  Processing: OTU.4291
  Processing: OTU.5849
  Processing: OTU.3192
  Processing: OTU.13806
  Processing: OTU.690
  Processing: OTU.4290
  Processing: OTU.5848
  Processing: OTU.3191
  Processing: OTU.4758
  Processing: OTU.13801
  Processing: OTU.4292
  Processing: OTU.691
  Processing: OTU.3190
  Processing: OTU.5047
  Processing: OTU.568
  Processing: OTU.924
  Processing: OTU.5691
  Processing: OTU.5696
  Processing: OTU.5046
  Processing: OTU.6838
  Processing: OTU.728
  Processing: OTU.5045
  Processing: OTU.5044
  Processing: OTU.5042
  Processing: OTU.5041
  Processing: OTU.5040

Simulating gradient fractions


In [36]:
!cd $workDir; \
    SIPSim gradient_fractions \
    comm.txt \
    > fracs.txt

Simulating an OTU table


In [37]:
!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.1528"
   taxon abs-abundance:  1057472
  Processing taxon: "OTU.270"
   taxon abs-abundance:  546083
  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.289"
   taxon abs-abundance:  739004
  Processing taxon: "OTU.8004"
   taxon abs-abundance:  422768
  Processing taxon: "OTU.843"
   taxon abs-abundance:  1046772
  Processing taxon: "OTU.5917"
   taxon abs-abundance:  334173
  Processing taxon: "OTU.386"
   taxon abs-abundance:  544468
  Processing taxon: "OTU.1128"
   taxon abs-abundance:  333473
  Processing taxon: "OTU.1010"
   taxon abs-abundance:  422418
  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.421"
   taxon abs-abundance:  1042147
  Processing taxon: "OTU.2144"
   taxon abs-abundance:  228531
  Processing taxon: "OTU.878"
   taxon abs-abundance:  276921
  Processing taxon: "OTU.6450"
   taxon abs-abundance:  541256
  Processing taxon: "OTU.550"
   taxon abs-abundance:  420623
  Processing taxon: "OTU.8003"
   taxon abs-abundance:  228474
  Processing taxon: "OTU.323"
   taxon abs-abundance:  331647
  Processing taxon: "OTU.179"
  Processing taxon: "OTU.8842"
   taxon abs-abundance:  731121
  Processing taxon: "OTU.16"
   taxon abs-abundance:  276817
   taxon abs-abundance:  1892173
  Processing taxon: "OTU.373"
   taxon abs-abundance:  227358
  Processing taxon: "OTU.669"
   taxon abs-abundance:  197093
  Processing taxon: "OTU.3358"
   taxon abs-abundance:  420354
  Processing taxon: "OTU.542"
   taxon abs-abundance:  275955
  Processing taxon: "OTU.233"
   taxon abs-abundance:  331479
  Processing taxon: "OTU.6407"
   taxon abs-abundance:  539895
  Processing taxon: "OTU.2372"
  Processing taxon: "OTU.2530"
   taxon abs-abundance:  196859
   taxon abs-abundance:  226790
  Processing taxon: "OTU.1638"
   taxon abs-abundance:  275383
  Processing taxon: "OTU.709"
   taxon abs-abundance:  196831
  Processing taxon: "OTU.13701"
   taxon abs-abundance:  226086
  Processing taxon: "OTU.103"
   taxon abs-abundance:  331210
  Processing taxon: "OTU.504"
   taxon abs-abundance:  170649
  Processing taxon: "OTU.190"
  Processing taxon: "OTU.6187"
   taxon abs-abundance:  418159
   taxon abs-abundance:  1034847
  Processing taxon: "OTU.4467"
   taxon abs-abundance:  728520
  Processing taxon: "OTU.192"
   taxon abs-abundance:  196204
  Processing taxon: "OTU.732"
   taxon abs-abundance:  170568
  Processing taxon: "OTU.4450"
  Processing taxon: "OTU.140"
   taxon abs-abundance:  275053
   taxon abs-abundance:  225650
  Processing taxon: "OTU.539"
   taxon abs-abundance:  538902
  Processing taxon: "OTU.419"
   taxon abs-abundance:  330075
  Processing taxon: "OTU.383"
   taxon abs-abundance:  195414
  Processing taxon: "OTU.509"
   taxon abs-abundance:  170467
  Processing taxon: "OTU.398"
   taxon abs-abundance:  225603
  Processing taxon: "OTU.714"
   taxon abs-abundance:  417476
  Processing taxon: "OTU.1412"
   taxon abs-abundance:  274889
  Processing taxon: "OTU.2923"
  Processing taxon: "OTU.530"
   taxon abs-abundance:  170331
   taxon abs-abundance:  195048
  Processing taxon: "OTU.414"
   taxon abs-abundance:  151696
  Processing taxon: "OTU.4996"
  Processing taxon: "OTU.748"
   taxon abs-abundance:  225502
   taxon abs-abundance:  328671
  Processing taxon: "OTU.8941"
  Processing taxon: "OTU.6102"
   taxon abs-abundance:  151691
   taxon abs-abundance:  170188
  Processing taxon: "OTU.473"
   taxon abs-abundance:  195037
  Processing taxon: "OTU.381"
   taxon abs-abundance:  274713
  Processing taxon: "OTU.11322"
   taxon abs-abundance:  536823
  Processing taxon: "OTU.153"
   taxon abs-abundance:  724724
  Processing taxon: "OTU.7834"
   taxon abs-abundance:  151285
  Processing taxon: "OTU.170"
  Processing taxon: "OTU.984"
  Processing taxon: "OTU.870"
   taxon abs-abundance:  416339
   taxon abs-abundance:  170154
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.841"
   taxon abs-abundance:  224736
   taxon abs-abundance:  170100
  Processing taxon: "OTU.1034"
   taxon abs-abundance:  194920
  Processing taxon: "OTU.316"
   taxon abs-abundance:  327705
  Processing taxon: "OTU.985"
   taxon abs-abundance:  151270
  Processing taxon: "OTU.371"
   taxon abs-abundance:  272221
  Processing taxon: "OTU.1127"
  Processing taxon: "OTU.7337"
  Processing taxon: "OTU.5241"
   taxon abs-abundance:  169724
   taxon abs-abundance:  132239
   taxon abs-abundance:  1030925
  Processing taxon: "OTU.3062"
   taxon abs-abundance:  224448
  Processing taxon: "OTU.3841"
   taxon abs-abundance:  194736
  Processing taxon: "OTU.758"
   taxon abs-abundance:  151028
  Processing taxon: "OTU.794"
   taxon abs-abundance:  132066
  Processing taxon: "OTU.284"
   taxon abs-abundance:  169661
  Processing taxon: "OTU.76"
   taxon abs-abundance:  1879774
  Processing taxon: "OTU.707"
  Processing taxon: "OTU.144"
   taxon abs-abundance:  414378
   taxon abs-abundance:  272065
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.474"
  Processing taxon: "OTU.317"
   taxon abs-abundance:  271944
   taxon abs-abundance:  531582
  Processing taxon: "OTU.399"
   taxon abs-abundance:  326985
  Processing taxon: "OTU.13643"
  Processing taxon: "OTU.231"
   taxon abs-abundance:  150979
   taxon abs-abundance:  194616
  Processing taxon: "OTU.900"
  Processing taxon: "OTU.305"
   taxon abs-abundance:  132032
   taxon abs-abundance:  224168
  Processing taxon: "OTU.1689"
   taxon abs-abundance:  169591
  Processing taxon: "OTU.658"
  Processing taxon: "OTU.664"
   taxon abs-abundance:  131880
   taxon abs-abundance:  150977
  Processing taxon: "OTU.123"
  Processing taxon: "OTU.4715"
  Processing taxon: "OTU.717"
   taxon abs-abundance:  721248
   taxon abs-abundance:  194086
   taxon abs-abundance:  116325
  Processing taxon: "OTU.453"
   taxon abs-abundance:  224066
  Processing taxon: "OTU.12647"
   taxon abs-abundance:  169123
  Processing taxon: "OTU.208"
   taxon abs-abundance:  271514
  Processing taxon: "OTU.2347"
   taxon abs-abundance:  131723
  Processing taxon: "OTU.853"
   taxon abs-abundance:  150755
  Processing taxon: "OTU.478"
  Processing taxon: "OTU.1702"
   taxon abs-abundance:  326510
   taxon abs-abundance:  116149
  Processing taxon: "OTU.9954"
  Processing taxon: "OTU.449"
   taxon abs-abundance:  413950
   taxon abs-abundance:  194033
  Processing taxon: "OTU.12448"
  Processing taxon: "OTU.3817"
   taxon abs-abundance:  131603
   taxon abs-abundance:  169046
  Processing taxon: "OTU.5904"
   taxon abs-abundance:  116074
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.2414"
   taxon abs-abundance:  116072
  Processing taxon: "OTU.874"
  Processing taxon: "OTU.3355"
   taxon abs-abundance:  150620
   taxon abs-abundance:  223749
  Processing taxon: "OTU.3228"
   taxon abs-abundance:  531080
  Processing taxon: "OTU.4938"
   taxon abs-abundance:  270909
  Processing taxon: "OTU.648"
   taxon abs-abundance:  131501
  Processing taxon: "OTU.6134"
   taxon abs-abundance:  115890
  Processing taxon: "OTU.1292"
  Processing taxon: "OTU.3886"
   taxon abs-abundance:  193871
   taxon abs-abundance:  168198
  Processing taxon: "OTU.756"
   taxon abs-abundance:  149974
  Processing taxon: "OTU.9497"
   taxon abs-abundance:  326118
  Processing taxon: "OTU.8572"
  Processing taxon: "OTU.2233"
  Processing taxon: "OTU.1270"
   taxon abs-abundance:  130557
   taxon abs-abundance:  223570
   taxon abs-abundance:  115861
  Processing taxon: "OTU.8712"
   taxon abs-abundance:  105277
  Processing taxon: "OTU.501"
   taxon abs-abundance:  1024914
  Processing taxon: "OTU.3398"
   taxon abs-abundance:  168102
  Processing taxon: "OTU.1489"
   taxon abs-abundance:  149397
  Processing taxon: "OTU.402"
   taxon abs-abundance:  192793
  Processing taxon: "OTU.331"
   taxon abs-abundance:  269637
  Processing taxon: "OTU.416"
  Processing taxon: "OTU.3519"
   taxon abs-abundance:  115686
   taxon abs-abundance:  412996
  Processing taxon: "OTU.298"
  Processing taxon: "OTU.2771"
   taxon abs-abundance:  130251
   taxon abs-abundance:  105258
  Processing taxon: "OTU.5428"
   taxon abs-abundance:  718679
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.406"
  Processing taxon: "OTU.483"
   taxon abs-abundance:  714772
   taxon abs-abundance:  223235
  Processing taxon: "OTU.774"
   taxon abs-abundance:  149025
  Processing taxon: "OTU.5367"
  Processing taxon: "OTU.350"
  Processing taxon: "OTU.12515"
   taxon abs-abundance:  168089
   taxon abs-abundance:  105040
   WARNING: No bins for taxon; likely caused by no BD KDE
   taxon abs-abundance:  115645
  Processing taxon: "OTU.4617"
   taxon abs-abundance:  104922
  Processing taxon: "OTU.515"
   taxon abs-abundance:  130213
  Processing taxon: "OTU.688"
   taxon abs-abundance:  326086
  Processing taxon: "OTU.6783"
   taxon abs-abundance:  192664
  Processing taxon: "OTU.8067"
   taxon abs-abundance:  529923
  Processing taxon: "OTU.2298"
   taxon abs-abundance:  104389
  Processing taxon: "OTU.973"
   taxon abs-abundance:  115352
  Processing taxon: "OTU.395"
  Processing taxon: "OTU.254"
   taxon abs-abundance:  269255
   taxon abs-abundance:  148885
  Processing taxon: "OTU.8534"
   taxon abs-abundance:  130058
  Processing taxon: "OTU.394"
   taxon abs-abundance:  168008
  Processing taxon: "OTU.637"
   taxon abs-abundance:  222862
  Processing taxon: "OTU.7306"
   taxon abs-abundance:  104389
  Processing taxon: "OTU.2584"
  Processing taxon: "OTU.426"
   taxon abs-abundance:  192547
   taxon abs-abundance:  114983
  Processing taxon: "OTU.2633"
   taxon abs-abundance:  95062
  Processing taxon: "OTU.344"
   taxon abs-abundance:  129452
  Processing taxon: "OTU.683"
  Processing taxon: "OTU.682"
   taxon abs-abundance:  148781
   taxon abs-abundance:  412719
  Processing taxon: "OTU.8126"
   taxon abs-abundance:  104389
  Processing taxon: "OTU.5635"
   taxon abs-abundance:  114949
  Processing taxon: "OTU.460"
  Processing taxon: "OTU.3642"
  Processing taxon: "OTU.1136"
   taxon abs-abundance:  325743
   taxon abs-abundance:  168004
   taxon abs-abundance:  95046
  Processing taxon: "OTU.689"
   taxon abs-abundance:  269013
  Processing taxon: "OTU.4943"
   taxon abs-abundance:  129175
  Processing taxon: "OTU.3083"
  Processing taxon: "OTU.897"
   taxon abs-abundance:  222767
  Processing taxon: "OTU.6192"
   taxon abs-abundance:  104051
   taxon abs-abundance:  192208
  Processing taxon: "OTU.492"
   taxon abs-abundance:  148466
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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:  48668
  Processing taxon: "OTU.7872"
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   WARNING: No bins for taxon; likely caused by no BD KDE
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  Processing taxon: "OTU.8424"
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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.8647"
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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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  Processing taxon: "OTU.12726"
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  Processing taxon: "OTU.2171"
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   WARNING: No bins for taxon; likely caused by no BD KDE
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  Processing taxon: "OTU.5909"
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  Processing taxon: "OTU.12199"
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  Processing taxon: "OTU.1876"
  Processing taxon: "OTU.13052"
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  Processing taxon: "OTU.8623"
  Processing taxon: "OTU.2560"
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  Processing taxon: "OTU.1195"
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  Processing taxon: "OTU.559"
   taxon abs-abundance:  280556
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.10167"
  Processing taxon: "OTU.1976"
   taxon abs-abundance:  279647
  Processing taxon: "OTU.4831"
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  Processing taxon: "OTU.6676"
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  Processing taxon: "OTU.3004"
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  Processing taxon: "OTU.7694"
  Processing taxon: "OTU.14091"
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   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1778"
  Processing taxon: "OTU.6637"
   taxon abs-abundance:  35665
   taxon abs-abundance:  37633
   taxon abs-abundance:  36807
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.4243"
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  Processing taxon: "OTU.4012"
  Processing taxon: "OTU.1138"
  Processing taxon: "OTU.14244"
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  Processing taxon: "OTU.9627"
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  Processing taxon: "OTU.9274"
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  Processing taxon: "OTU.1879"
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  Processing taxon: "OTU.5683"
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   taxon abs-abundance:  34908
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  Processing taxon: "OTU.4432"
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  Processing taxon: "OTU.1599"
  Processing taxon: "OTU.359"
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   taxon abs-abundance:  647913
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  Processing taxon: "OT