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 [16]:
workDir = '/home/nick/notebook/SIPSim/dev/priming_exp/validation_sample/X12C.700.28_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 =  6896
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.700.28_frac_OTU.txt')

# misc
nprocs = 20

Init


In [17]:
import glob
import cPickle as pickle
import copy
from IPython.display import Image

In [18]:
%load_ext rpy2.ipython


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

In [19]:
%%R
library(ggplot2)
library(dplyr)
library(tidyr)
library(gridExtra)

In [20]:
if not os.path.isdir(workDir):
    os.makedirs(workDir)

Creating a community file from the fraction relative abundances


In [21]:
%%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     1.502396379       1.667181645     1.97331895 X12C.700.28
2    OTU.10     0.166895317       0.167189912     0.34949460 X12C.700.28
3   OTU.100     0.179099861       0.156171401     0.44673472 X12C.700.28
4  OTU.1000     0.005144254       0.003672572     0.01243420 X12C.700.28
5 OTU.10000     0.003698954       0.002475258     0.01027925 X12C.700.28
6  OTU.1001     0.011117285       0.012205991     0.02067802 X12C.700.28

In [22]:
%%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       1.502396       1    1
2      OTU.2       1.260967       1    2
3      OTU.4       1.212520       1    3
4      OTU.9       1.132359       1    4
5      OTU.3       1.085465       1    5
6     OTU.22       1.073704       1    6

In [23]:
%%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      1.2629124    1
2       1      OTU.2      1.0599675    2
3       1      OTU.4      1.0192425    3
4       1      OTU.9      0.9518592    4
5       1      OTU.3      0.9124408    5
6       1     OTU.22      0.9025540    6

In [24]:
%%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: 6896 
Community richness = number of OTUs?   TRUE 

In [25]:
%%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 [26]:
%%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      1.2629124    1
2       1      OTU.2      1.0599675    2
3       1      OTU.4      1.0192425    3
4       1      OTU.9      0.9518592    4
5       1      OTU.3      0.9124408    5
6       1     OTU.22      0.9025540    6

In [27]:
%%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 [28]:
%%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] 6896
  library taxon_name rel_abund_perc rank
1       1      OTU.1       1.262912    1
2       1      OTU.2       1.059967    2
3       1      OTU.4       1.019242    3

In [29]:
%%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 [30]:
%%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 [31]:
%%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 [32]:
%%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:  192 
-------- 
       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    0.003295660 3860
2 CP001738_Thermomonospora_curvata_DSM_43183       1    0.003758724 3414
3 CP001738_Thermomonospora_curvata_DSM_43183       1    0.010023752 1344

In [33]:
%%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 [34]:
%%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 [35]:
!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 [36]:
%%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 [37]:
%%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:  6704 
---------
  library taxon_name rel_abund_perc rank
1       1   OTU.9845   0.0009148378 6896
2       1   OTU.9632   0.0009148378 6895
3       1   OTU.9463   0.0009148378 6894
4       1   OTU.9372   0.0009148378 6893
5       1   OTU.8972   0.0009148378 6892

In [38]:
%%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 [39]:
%%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 [40]:
# 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: 6704
Out[40]:
['OTU.9845', 'OTU.9632', 'OTU.9463', 'OTU.9372']

In [41]:
# 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: 192

In [42]:
# 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 [43]:
# 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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,138,90,59,73,162,140,164,104,72,162,143,148,116,141,60,18,2,99,34,57,63,105,138,56,162,127,173,11,80,152,139,96,171,111,186,118,15,156,14,171,83,130,35,15,38,61,19,156,9,48,186,74,30,7,11,58,114,136,162,90,71,109,157,26,75,84,1,128,53,143,170,18,32,84,14,58,26,132,54,127,63,82,45,111,29,16,63,78,26,74,165,99,65,145,179,127,15,129,107,132,8,105,105,127,166,142,160,37,28,109,28,109,1,133,6,3,111,10,67,51,160,92,141,156,83,45,174,178,28,75,157,116,85,22,142,53,179,28,157,107,157,65,19,69,56,91,37,16,190,3,102,169,145,94,39,168,3,49,31,137,20,173,181,158,53,39,12,69,21,57,160,177,37,136,18,122,30,104,34,96,142,89,169,92,153,13,177,29,166,151,159,49,99,94,76,90,6,91,42,23,74,87,15,8,167,157,20,125,110,91,6,47,183,60,154,127,39,48,47,83,89,124,114,80,39,123,186,7,96,190,96,126,180,19,168,5,13,111,50,16,31,38,114,44,34,75,87,105,120,65,75,107,7,38,175,30,80,153,188,106,50,191,116,133,5,136,44,187,104,76,43,150,39,94,91,179,69,57,117,70,24,108,179,16,86,166,155,143,97,167,169,183,76,23,29,164,49,123,110,23,157,134,17,148,90,172,155,40,42,10,114,47,149,88,169,45,6,188,166,150,10,80,118,180,138,153,136,6,155,116,106,10,178,180,172,56,59,113,40,14,180,145,112,148,7,174,191,104,102,185,105,113,151,174,55,67,60,83,77,34,35,21,38,168,26,63,87,5,155,122,103,63,178,36,31,171,144,135,113,20,49,175,29,86,187,86,80,190,190,34,175,2,72,171,37,139,155,147,168,22,146,68,13,145,98,18,137,90,123,103,22,191,64,11,20,30,66,13,187,10,158,93,55,99,181,126,7,118,94,92,171,133,21,79,127,137,71,63,126,33,6,28,11,57,8,18,70,173,128,167,40,78,130,99,95,69,104,87,10,98,35,22,80,76,119,100,154,18,20,76,103,92,40,123,130,22,124,46,47,84,52,94,41,163,11,160,191,146,80,31,141,54,100,36,27,15,24,130,120,98,7,114,113,165,108,24,64,182,8,80,145,164,148,2,153,172,167,139,160,165,187,154,98,12,62,123,166,56,61,191,178,74,164,146,19,7,106,70,190,71,101,0,42,130,107,115,108,12,18,77,23,106,184,171,96,12,118,147,56,129,189,27,118,61,65,92,10,112,64,51,89,62,18,168,114,161,183,189,118,23,3,128,61,35,102,164,162,32,2,76,117,38,27,131,20,142,156,94,99,190,185,63,53,87,134,124,86,139,42,133,151,104,57,119,71,170,76,27,191,167,137,62,36,20,189,26,100,66,28,168,85,104,28,108,102,54,124,96,26,23,55,8,175,99,113,135,135,27,61,69,60,162,163,186,29,30,101,50,167,89,141,175,84,23,85,34,149,56,111,20,97,60,27,160,94,5,159,105,41,40,191,172,146,44,138,88,107,36,122,132,141,112,25,76,56,40,67,154,171,181,169,48,58,179,5,44,5,182,189,169,139,155,190,159,182,14,104,13,67,135,68,139,97,30,170,111,97,181,8,189,186,1,171,168,86,182,126,123,120,182,71,17,96,4,178,36,115,135,0,186,83,157,159,106,67,30,13,32,41,177,145,41,133,88,169,58,102,167,173,25,153,95,86,158,102,117,64,62,182,161,87,43,184,167,187,129,128,32,105,67,172,48,118,32,64,161,151,120,32,70,187,38,102,129,120,127,52,23,163,56,166,29,152,137,35,124,161,54,55,88,132,36,83,133,122,78,5,11,32,33,42,2,175,191,122,178,80,163,135,49,54,142,90,10,23,158,101,141,134,81,190,95,113,109,67,101,7,56,125,12,152,109,100,41,135,95,68,181,53,161,100,125,130,166,74,7,136,22,106,10,14,59,101,148,21,56,52,106,114,29,53,62,169,67,59,82,127,186,6,7,20,152,165,180,135,59,64,4,128,61,21,77,167,105,11,156,142,14,175,143,49,156,95,86,149,174,75,1,136,61,88,123,16,6,118,185,112,155,132,115,166,22,138,141,181,68,102,50,186,123,98,78,78,128,162,175,124,23,115,129,52,165,123,76,89,157,112,159,51,36,71,1,161,107,78,41,1,155,32,189,112,160,180,171,15,69,82,13,99,185,85,56,144,76,85,100,67,45,188,118,162,118,125,136,185,132,115,125,120,129,6,74,25,5,55,29,38,87,141,45,83,161,101,6,128,76,169,32,162,169,84,165,19,8,116,12,126,95,94,19,68,97,21,122,156,179,10,169,187,156,66,97,181,85,75,190,153,10,139,39,95,60,82,166,15,146,20,101,88,78,36,44,57,175,179,114,190,155,128,70,159,49,105,7,81,31,25,101,4,80,184,176,8,73,70,59,126,148,80,62,55,188,38,16,11,80,127,99,186,130,1,50,94,102,10,141,29,94,26,82,84,130,162,26,72,44,109,126,47,15,102,162,91,138,38,126,186,58,47,100,45,62,174,177,38,90,78,45,29,166,97,9,166,169,119,178,95,42,75,41,169,120,130,24,12,132,0,45,143,7,190,48,185,154,170,137,94,8,69,53,80,33,157,9,100,186,154,137,96,184,19,5,146,165,58,31,12,122,133,36,56,183,27,126,108,163,32,36,104,153,50,132,172,175,165,176,58,74,173,143,98,63,76,178,76,133,114,132,76,184,138,63,37,65,39,17,44,102,115,72,112,106,54,58,2,81,55,76,187,152,123,26,64,150,127,158,102,152,24,145,126,83,185,54,168,127,63,69,17,3,54,182,43,55,46,180,157,47,189,57,181,17,153,180,70,158,163,176,158,46,139,167,48,173,108,173,151,174,177,120,50,40,144,184,153,105,79,76,118,115,91,22,176,48,71,89,179,62,0,3,3,76,190,56,128,73,164,133,147,127,125,50,186,153,173,124,149,94,172,57,172,85,114,42,132,97,104,79,127,167,154,108,124,115,3,101,31,115,141,51,60,40,149,33,20,146,49,25,65,99,164,61,13,10,108,21,32,50,152,50,59,108,110,46,136,145,90,49,170,18,39,124,30,147,44,21,70,116,37,29,40,31,189,61,73,54,80,157,126,158,152,146,151,162,144,27,95,3,144,70,109,173,80,83,51,92,73,154,164,107,63,67,32,102,19,112,23,175,120,188,84,49,52,156,88,190,135,43,128,94,135,6,105,41,91,74,35,26,137,103,91,173,33,149,30,19,95,23,161,171,6,0,66,104,154,1,114,22,4,176,188,42,188,126,189,94,180,164,67,31,71,72,120,4,101,62,61,120,154,167,55,75,78,66,97,22,157,0,191,47,103,107,50,35,37,180,59,71,116,57,149,38,78,20,15,181,180,179,32,33,123,166,39,116,103,53,115,16,154,171,116,50,111,11,154,131,25,20,17,130,137,164,185,109,105,182,74,40,11,55,17,17,123,128,131,38,167,95,26,178,135,94,73,174,191,47,5,174,160,60,6,47,187,76,22,16,87,4,35,68,154,51,75,154,163,187,109,55,92,69,119,149,114,80,1,148,174,172,150,156,25,74,16,163,26,3,115,146,148,106,128,76,156,14,55,191,167,157,15,139,4,68,63,118,175,81,121,107,168,1,55,7,93,72,66,74,160,132,147,150,169,139,29,134,161,188,77,67,165,138,88,99,76,137,152,49,99,71,71,16,155,167,146,58,38,58,140,19,8,7,156,127,108,119,151,135,162,59,151,175,68,83,8,133,35,149,191,12,13,35,68,23,148,25,81,41,5,96,148,154,129,112,30,18,184,68,163,81,125,78,69,68,187,151,16,150,186,73,164,177,154,75,152,88,109,167,144,98,57,134,73,17,67,152,146,61,18,178,94,185,188,191,6,181,102,150,98,140,10,0,26,30,74,2,189,54,107,30,79,36,96,145,151,90,66,4,29,141,77,147,3,97,58,148,185,184,65,96,27,102,79,90,118,57,109,1,107,119,7,149,19,131,166,50,115,128,68,163,168,187,157,185,94,95,129,61,11,57,169,175,158,88,63,166,54,131,104,23,39,6,46,166,90,45,181,158,85,88,74,44,44,19,97,86,150,12,6,145,121,168,138,65,28,72,8,29,126,158,44,50,173,50,53,44,38,24,145,146,162,115,145,166,5,177,105,9,84,149,59,96,147,3,136,4,104,113,172,59,9,134,148,152,102,82,186,40,119,103,0,120,109,183,13,171,49,183,161,5,52,189,76,17,21,163,178,151,65,65,60,146,29,66,100,78,162,13,14,94,50,35,137,89,63,119,66,116,8,60,10,17,136,33,177,29,10,5,177,81,11,41,30,167,38,130,169,3,46,15,48,106,71,169,154,76,11,150,160,85,64,66,27,151,177,182,23,174,102,47,159,13,0,77,117,95,0,83,173,30,88,100,146,185,179,190,4,157,74,107,157,171,36,30,151,166,68,129,150,17,154,91,87,91,0,99,23,107,85,34,110,120,34,109,15,179,113,40,144,69,95,54,13,53,105,47,152,33,29,80,25,104,121,141,145,96,73,23,28,65,106,98,172,187,147,31,75,44,25,151,143,128,173,7,183,140,167,50,60,125,183,148,153,77,90,156,107,26,69,96,124,168,36,71,163,148,109,48,151,20,190,34,37,94,87,112,50,178,11,0,56,9,88,60,162,44,136,9,145,17,77,111,123,78,151,103,8,0,125,108,146,136,151,12,23,162,114,98,186,173,25,81,109,73,68,145,101,110,29,172,132,166,171,150,65,82,112,174,133,170,39,77,97,100,159,148,69,81,78,149,161,130,133,71,101,77,59,126,186,120,152,160,40,89,121,119,1,49,132,184,99,54,156,133,66,175,77,25,88,128,185,2,127,145,0,162,47,91,32,76,166,22,154,159,27,104,34,3,183,79,17,110,81,63,49,112,126,131,57,42,125,11,113,137,39,158,20,171,3,85,51,125,144,117,41,135,78,178,184,50,138,90,16,83,182,188,177,175,97,7,13,124,59,132,23,47,132,51,95,21,165,50,153,185,165,171,42,119,54,130,32,77,167,66,99,64,167,175,109,113,158,114,0,28,15,160,157,130,13,156,110,80,128,41,191,137,189,168,38,124,102,97,145,103,79,176,71,187,18,59,94,59,180,85,52,35,49,189,68,116,72,86,104,183,36,141,
Number of random taxa needed to reach richness: 6704

In [44]:
# renaming randomly selected KDEs by non-target OTU-ID
for i in range(len(ampFrag_rand)):
    ampFrag_rand[i][0] = nonTarget[i]

In [45]:
# 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: 6896

Converting fragments to kde object


In [46]:
!cd $workDir; \
    SIPSim fragment_kde \
    ampFrags_wRand.pkl \
    > ampFrags_wRand_kde.pkl

Adding diffusion


In [47]:
!cd $workDir; \
    SIPSim diffusion \
    ampFrags_wRand_kde.pkl \
    --np $nprocs \
    > ampFrags_wRand_kde_dif.pkl


Processing: OTU.759
Processing: OTU.2006
Processing: OTU.1525
Processing: OTU.5686
Processing: OTU.7815
Processing: OTU.2555
Processing: OTU.500
Processing: OTU.1526
Processing: OTU.1745
Processing: OTU.9017
Processing: OTU.2556
Processing: OTU.587
Processing: OTU.4371
Processing: OTU.501
Processing: OTU.7047
Processing: OTU.1527
Processing: OTU.1746
Processing: OTU.1322
Processing: OTU.9272
Processing: OTU.2557
Processing: OTU.7818
Processing: OTU.4376
Processing: OTU.6892
Processing: OTU.508
Processing: OTU.7046
Processing: OTU.1520
Processing: OTU.1521
Processing: OTU.1374
Processing: OTU.5901
Processing: OTU.1323
Processing: OTU.9274
Processing: OTU.296
Processing: OTU.4354
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Making an incorp config file


In [48]:
!cd $workDir; \
    SIPSim incorpConfigExample \
    --percTaxa 0 \
    --percIncorpUnif 100 \
    > PT0_PI100.config

Adding isotope incorporation to BD distribution


In [49]:
!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 [50]:
!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.1424
  Processing: OTU.3719
  Processing: OTU.3396
  Processing: OTU.1051
  Processing: OTU.1353
  Processing: OTU.12621
  Processing: OTU.1564
  Processing: OTU.7950
  Processing: OTU.1427
  Processing: OTU.569
  Processing: OTU.39
  Processing: OTU.6253
  Processing: OTU.1352
  Processing: OTU.12194
  Processing: OTU.4085
  Processing: OTU.11
  Processing: OTU.1548
  Processing: OTU.38
  Processing: OTU.6290
  Processing: OTU.6251
  Processing: OTU.4271
  Processing: OTU.4737
  Processing: OTU.1566
  Processing: OTU.10
  Processing: OTU.1549
  Processing: OTU.32
  Processing: OTU.7402
  Processing: OTU.6250
  Processing: OTU.1350
  Processing: OTU.12196
  Processing: OTU.4087
  Processing: OTU.13
  Processing: OTU.1546
  Processing: OTU.667
  Processing: OTU.4277
  Processing: OTU.6257
  Processing: OTU.1927
  Processing: OTU.5549
  Processing: OTU.1544
  Processing: OTU.12
  Processing: OTU.443
  Processing: OTU.1356
  Processing: OTU.6256
  Processing: OTU.1928
  Processing: OTU.1929
  Processing: OTU.4106
  Processing: OTU.6021
  Processing: OTU.15
  Processing: OTU.14
  Processing: OTU.1355
  Processing: OTU.666
  Processing: OTU.6255
  Processing: OTU.4738
  Processing: OTU.1542
  Processing: OTU.3502
  Processing: OTU.17
  Processing: OTU.1354
  Processing: OTU.6135
  Processing: OTU.10188
  Processing: OTU.1543
  Processing: OTU.4739
  Processing: OTU.6023
  Processing: OTU.16
  Processing: OTU.4279
  Processing: OTU.442
  Processing: OTU.7028
  Processing: OTU.400
  Processing: OTU.3504
  Processing: OTU.6120
  Processing: OTU.6018
  Processing: OTU.7022
  Processing: OTU.6591
  Processing: OTU.6025
  Processing: OTU.5865
  Processing: OTU.7020
  Processing: OTU.3506
  Processing: OTU.441
  Processing: OTU.3524
  Processing: OTU.3059

Simulating gradient fractions


In [51]:
!cd $workDir; \
    SIPSim gradient_fractions \
    comm.txt \
    > fracs.txt

Simulating an OTU table


In [52]:
!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:  12629124
  Processing taxon: "OTU.48"
   taxon abs-abundance:  1836383
  Processing taxon: "OTU.4164"
   taxon abs-abundance:  1065314
  Processing taxon: "OTU.193"
   taxon abs-abundance:  711452
  Processing taxon: "OTU.7805"
   taxon abs-abundance:  527869
  Processing taxon: "OTU.509"
   taxon abs-abundance:  401332
  Processing taxon: "OTU.12094"
   taxon abs-abundance:  322287
  Processing taxon: "OTU.309"
   taxon abs-abundance:  400944
  Processing taxon: "OTU.6187"
   taxon abs-abundance:  524961
  Processing taxon: "OTU.402"
   taxon abs-abundance:  321573
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.293"
   taxon abs-abundance:  321440
  Processing taxon: "OTU.7738"
   taxon abs-abundance:  704612
  Processing taxon: "OTU.674"
   taxon abs-abundance:  398769
  Processing taxon: "OTU.472"
   taxon abs-abundance:  264515
  Processing taxon: "OTU.968"
   taxon abs-abundance:  321289
  Processing taxon: "OTU.134"
   taxon abs-abundance:  1046600
  Processing taxon: "OTU.3519"
   taxon abs-abundance:  524686
  Processing taxon: "OTU.6962"
  Processing taxon: "OTU.6823"
   taxon abs-abundance:  263889
   taxon abs-abundance:  398434
  Processing taxon: "OTU.391"
   taxon abs-abundance:  321282
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.918"
   taxon abs-abundance:  321069
  Processing taxon: "OTU.107"
   taxon abs-abundance:  704377
  Processing taxon: "OTU.415"
   taxon abs-abundance:  263270
  Processing taxon: "OTU.565"
   taxon abs-abundance:  226083
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.825"
   taxon abs-abundance:  226060
  Processing taxon: "OTU.7606"
   taxon abs-abundance:  394582
  Processing taxon: "OTU.771"
   taxon abs-abundance:  522897
  Processing taxon: "OTU.416"
   taxon abs-abundance:  318694
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.400"
   taxon abs-abundance:  318616
  Processing taxon: "OTU.160"
  Processing taxon: "OTU.422"
   taxon abs-abundance:  1833807
   taxon abs-abundance:  263158
  Processing taxon: "OTU.7953"
   taxon abs-abundance:  225880
  Processing taxon: "OTU.315"
   taxon abs-abundance:  225794
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.2281"
   taxon abs-abundance:  225224
  Processing taxon: "OTU.490"
   taxon abs-abundance:  393874
  Processing taxon: "OTU.1999"
   taxon abs-abundance:  262920
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.300"
   taxon abs-abundance:  262897
  Processing taxon: "OTU.744"
   taxon abs-abundance:  318037
  Processing taxon: "OTU.952"
   taxon abs-abundance:  196086
  Processing taxon: "OTU.631"
   taxon abs-abundance:  1044252
  Processing taxon: "OTU.6217"
   taxon abs-abundance:  697689
  Processing taxon: "OTU.219"
   taxon abs-abundance:  521875
  Processing taxon: "OTU.1814"
   taxon abs-abundance:  225127
  Processing taxon: "OTU.642"
   taxon abs-abundance:  262854
  Processing taxon: "OTU.398"
   taxon abs-abundance:  195880
  Processing taxon: "OTU.479"
   taxon abs-abundance:  314846
  Processing taxon: "OTU.8096"
   taxon abs-abundance:  392895
  Processing taxon: "OTU.960"
   taxon abs-abundance:  224977
  Processing taxon: "OTU.1009"
   taxon abs-abundance:  195879
  Processing taxon: "OTU.735"
   taxon abs-abundance:  262484
  Processing taxon: "OTU.307"
   taxon abs-abundance:  224434
  Processing taxon: "OTU.722"
  Processing taxon: "OTU.662"
   taxon abs-abundance:  313795
   taxon abs-abundance:  173597
  Processing taxon: "OTU.5552"
   taxon abs-abundance:  195529
  Processing taxon: "OTU.5018"
   taxon abs-abundance:  520991
  Processing taxon: "OTU.209"
   taxon abs-abundance:  392810
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.248"
   taxon abs-abundance:  391294
  Processing taxon: "OTU.434"
   taxon abs-abundance:  262094
  Processing taxon: "OTU.885"
   taxon abs-abundance:  173370
  Processing taxon: "OTU.239"
   taxon abs-abundance:  694991
  Processing taxon: "OTU.1954"
  Processing taxon: "OTU.10065"
   taxon abs-abundance:  195438
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.7834"
   taxon abs-abundance:  224100
   taxon abs-abundance:  195395
  Processing taxon: "OTU.417"
   taxon abs-abundance:  313773
  Processing taxon: "OTU.1110"
   taxon abs-abundance:  173190
  Processing taxon: "OTU.535"
   taxon abs-abundance:  261663
  Processing taxon: "OTU.573"
   taxon abs-abundance:  195352
  Processing taxon: "OTU.2489"
   taxon abs-abundance:  224096
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1628"
   taxon abs-abundance:  222931
  Processing taxon: "OTU.6439"
  Processing taxon: "OTU.7773"
   taxon abs-abundance:  1042079
   taxon abs-abundance:  390577
  Processing taxon: "OTU.8534"
   taxon abs-abundance:  172914
  Processing taxon: "OTU.143"
   taxon abs-abundance:  519433
  Processing taxon: "OTU.653"
   taxon abs-abundance:  155361
  Processing taxon: "OTU.3922"
   taxon abs-abundance:  195176
  Processing taxon: "OTU.3730"
   taxon abs-abundance:  312763
  Processing taxon: "OTU.6074"
   taxon abs-abundance:  261472
  Processing taxon: "OTU.871"
   taxon abs-abundance:  222863
  Processing taxon: "OTU.1017"
   taxon abs-abundance:  172870
  Processing taxon: "OTU.805"
   taxon abs-abundance:  154877
  Processing taxon: "OTU.7315"
   taxon abs-abundance:  195143
  Processing taxon: "OTU.169"
  Processing taxon: "OTU.10167"
   taxon abs-abundance:  691061
   taxon abs-abundance:  390015
  Processing taxon: "OTU.5857"
   taxon abs-abundance:  172674
  Processing taxon: "OTU.381"
  Processing taxon: "OTU.1597"
   taxon abs-abundance:  222746
   taxon abs-abundance:  1832370
  Processing taxon: "OTU.4544"
   taxon abs-abundance:  154875
  Processing taxon: "OTU.4133"
   taxon abs-abundance:  261259
  Processing taxon: "OTU.366"
   taxon abs-abundance:  312232
  Processing taxon: "OTU.1010"
   taxon abs-abundance:  194871
  Processing taxon: "OTU.626"
  Processing taxon: "OTU.578"
   taxon abs-abundance:  172584
   taxon abs-abundance:  154696
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.5356"
   taxon abs-abundance:  172510
  Processing taxon: "OTU.656"
   taxon abs-abundance:  519165
  Processing taxon: "OTU.202"
   taxon abs-abundance:  222561
  Processing taxon: "OTU.427"
   taxon abs-abundance:  261200
  Processing taxon: "OTU.596"
   taxon abs-abundance:  194664
  Processing taxon: "OTU.7573"
   taxon abs-abundance:  154261
  Processing taxon: "OTU.1212"
   taxon abs-abundance:  138364
  Processing taxon: "OTU.724"
   taxon abs-abundance:  172294
  Processing taxon: "OTU.602"
   taxon abs-abundance:  311607
  Processing taxon: "OTU.4374"
   taxon abs-abundance:  387467
  Processing taxon: "OTU.316"
   taxon abs-abundance:  221790
  Processing taxon: "OTU.555"
  Processing taxon: "OTU.7198"
   taxon abs-abundance:  138258
   taxon abs-abundance:  153695
  Processing taxon: "OTU.964"
   taxon abs-abundance:  194109
  Processing taxon: "OTU.546"
   taxon abs-abundance:  172215
  Processing taxon: "OTU.6013"
   taxon abs-abundance:  259876
  Processing taxon: "OTU.5262"
  Processing taxon: "OTU.9454"
   taxon abs-abundance:  1033212
   taxon abs-abundance:  137842
  Processing taxon: "OTU.6443"
   taxon abs-abundance:  153368
  Processing taxon: "OTU.151"
  Processing taxon: "OTU.257"
   taxon abs-abundance:  311535
   taxon abs-abundance:  690862
  Processing taxon: "OTU.5378"
   taxon abs-abundance:  221437
  Processing taxon: "OTU.455"
   taxon abs-abundance:  172165
  Processing taxon: "OTU.582"
  Processing taxon: "OTU.6407"
   taxon abs-abundance:  193923
   taxon abs-abundance:  517282
  Processing taxon: "OTU.394"
  Processing taxon: "OTU.466"
   taxon abs-abundance:  387060
   taxon abs-abundance:  137618
  Processing taxon: "OTU.636"
   taxon abs-abundance:  153315
  Processing taxon: "OTU.330"
   taxon abs-abundance:  259796
  Processing taxon: "OTU.902"
   taxon abs-abundance:  171574
  Processing taxon: "OTU.864"
  Processing taxon: "OTU.489"
   taxon abs-abundance:  193789
   taxon abs-abundance:  137545
  Processing taxon: "OTU.6354"
   taxon abs-abundance:  220812
  Processing taxon: "OTU.831"
   taxon abs-abundance:  152937
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1098"
   taxon abs-abundance:  152276
  Processing taxon: "OTU.1518"
   taxon abs-abundance:  125117
  Processing taxon: "OTU.485"
   taxon abs-abundance:  311226
  Processing taxon: "OTU.971"
  Processing taxon: "OTU.8842"
   taxon abs-abundance:  137362
   taxon abs-abundance:  170875
  Processing taxon: "OTU.7837"
   taxon abs-abundance:  259222
  Processing taxon: "OTU.5238"
   taxon abs-abundance:  193744
  Processing taxon: "OTU.966"
   taxon abs-abundance:  152164
  Processing taxon: "OTU.627"
   taxon abs-abundance:  124928
  Processing taxon: "OTU.664"
   taxon abs-abundance:  220808
  Processing taxon: "OTU.264"
   taxon abs-abundance:  387032
  Processing taxon: "OTU.1480"
   taxon abs-abundance:  137150
  Processing taxon: "OTU.1093"
   taxon abs-abundance:  170443
  Processing taxon: "OTU.470"
   taxon abs-abundance:  512922
  Processing taxon: "OTU.826"
   taxon abs-abundance:  124632
  Processing taxon: "OTU.954"
   taxon abs-abundance:  151672
  Processing taxon: "OTU.702"
   taxon abs-abundance:  193553
  Processing taxon: "OTU.324"
   taxon abs-abundance:  311000
  Processing taxon: "OTU.11818"
   taxon abs-abundance:  136476
  Processing taxon: "OTU.751"
   taxon abs-abundance:  258958
  Processing taxon: "OTU.6205"
   taxon abs-abundance:  220685
  Processing taxon: "OTU.405"
  Processing taxon: "OTU.7249"
   taxon abs-abundance:  687939
   taxon abs-abundance:  124398
  Processing taxon: "OTU.245"
   taxon abs-abundance:  170429
  Processing taxon: "OTU.1039"
   taxon abs-abundance:  151670
  Processing taxon: "OTU.934"
   taxon abs-abundance:  136419
  Processing taxon: "OTU.482"
   taxon abs-abundance:  192739
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.4957"
  Processing taxon: "OTU.468"
   taxon abs-abundance:  192736
   taxon abs-abundance:  124153
  Processing taxon: "OTU.198"
   taxon abs-abundance:  386124
  Processing taxon: "OTU.388"
  Processing taxon: "OTU.4934"
   taxon abs-abundance:  170243
   taxon abs-abundance:  151569
  Processing taxon: "OTU.721"
   taxon abs-abundance:  220387
  Processing taxon: "OTU.231"
   taxon abs-abundance:  257961
  Processing taxon: "OTU.2158"
   taxon abs-abundance:  136327
  Processing taxon: "OTU.700"
   taxon abs-abundance:  112514
  Processing taxon: "OTU.938"
  Processing taxon: "OTU.254"
   taxon abs-abundance:  123672
   taxon abs-abundance:  310972
  Processing taxon: "OTU.90"
   taxon abs-abundance:  1032992
  Processing taxon: "OTU.8895"
   taxon abs-abundance:  191957
  Processing taxon: "OTU.4328"
   taxon abs-abundance:  151565
  Processing taxon: "OTU.8616"
   taxon abs-abundance:  112503
  Processing taxon: "OTU.6149"
   taxon abs-abundance:  136307
  Processing taxon: "OTU.5838"
  Processing taxon: "OTU.4025"
   taxon abs-abundance:  169948
  Processing taxon: "OTU.4922"
   taxon abs-abundance:  123595
   taxon abs-abundance:  509026
  Processing taxon: "OTU.619"
   taxon abs-abundance:  219819
  Processing taxon: "OTU.65"
   taxon abs-abundance:  1824002
  Processing taxon: "OTU.762"
  Processing taxon: "OTU.322"
   taxon abs-abundance:  112287
   taxon abs-abundance:  256247
  Processing taxon: "OTU.9017"
  Processing taxon: "OTU.5165"
   taxon abs-abundance:  123344
  Processing taxon: "OTU.637"
   taxon abs-abundance:  136228
  Processing taxon: "OTU.11361"
   taxon abs-abundance:  151478
   taxon abs-abundance:  191547
  Processing taxon: "OTU.214"
   taxon abs-abundance:  385965
  Processing taxon: "OTU.11751"
   taxon abs-abundance:  169878
  Processing taxon: "OTU.598"
   taxon abs-abundance:  309166
  Processing taxon: "OTU.1452"
   taxon abs-abundance:  112160
  Processing taxon: "OTU.941"
   taxon abs-abundance:  123194
  Processing taxon: "OTU.1433"
   taxon abs-abundance:  136223
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.1969"
  Processing taxon: "OTU.6130"
   taxon abs-abundance:  135927
   taxon abs-abundance:  219393
  Processing taxon: "OTU.961"
   taxon abs-abundance:  150710
  Processing taxon: "OTU.166"
   taxon abs-abundance:  687267
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.3368"
   taxon abs-abundance:  684737
  Processing taxon: "OTU.7827"
  Processing taxon: "OTU.3312"
   taxon abs-abundance:  191433
   taxon abs-abundance:  112155
  Processing taxon: "OTU.734"
   taxon abs-abundance:  169804
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.739"
   taxon abs-abundance:  169605
  Processing taxon: "OTU.819"
   taxon abs-abundance:  255960
  Processing taxon: "OTU.13967"
   taxon abs-abundance:  123136
  Processing taxon: "OTU.3799"
   taxon abs-abundance:  135800
  Processing taxon: "OTU.681"
   taxon abs-abundance:  103571
  Processing taxon: "OTU.6577"
   taxon abs-abundance:  150467
  Processing taxon: "OTU.1034"
   taxon abs-abundance:  112047
  Processing taxon: "OTU.383"
  Processing taxon: "OTU.12754"
   taxon abs-abundance:  308787
   taxon abs-abundance:  219252
  Processing taxon: "OTU.5408"
   taxon abs-abundance:  123129
  Processing taxon: "OTU.276"
   taxon abs-abundance:  508234
  Processing taxon: "OTU.1058"
   taxon abs-abundance:  169595
  Processing taxon: "OTU.1510"
  Processing taxon: "OTU.667"
  Processing taxon: "OTU.5674"
   taxon abs-abundance:  103520
   taxon abs-abundance:  191384
  Processing taxon: "OTU.500"
   taxon abs-abundance:  385360
   taxon abs-abundance:  135466
  Processing taxon: "OTU.2195"
   taxon abs-abundance:  112010
  Processing taxon: "OTU.516"
   taxon abs-abundance:  150137
  Processing taxon: "OTU.1638"
  Processing taxon: "OTU.607"
   taxon abs-abundance:  255275
   taxon abs-abundance:  123001
  Processing taxon: "OTU.458"
   taxon abs-abundance:  103516
  Processing taxon: "OTU.655"
   taxon abs-abundance:  111894
  Processing taxon: "OTU.1164"
   taxon abs-abundance:  135447
  Processing taxon: "OTU.5294"
   taxon abs-abundance:  169592
  Processing taxon: "OTU.306"
   taxon abs-abundance:  217637
  Processing taxon: "OTU.346"
  Processing taxon: "OTU.496"
   taxon abs-abundance:  191139
   taxon abs-abundance:  150122
  Processing taxon: "OTU.7851"
  Processing taxon: "OTU.708"
   taxon abs-abundance:  122937
   taxon abs-abundance:  103504
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.7275"
   taxon abs-abundance:  122929
  Processing taxon: "OTU.7938"
   taxon abs-abundance:  111848
  Processing taxon: "OTU.467"
   taxon abs-abundance:  307976
  Processing taxon: "OTU.663"
   taxon abs-abundance:  135420
  Processing taxon: "OTU.13643"
   taxon abs-abundance:  103292
  Processing taxon: "OTU.11122"
   taxon abs-abundance:  169536
  Processing taxon: "OTU.683"
  Processing taxon: "OTU.6002"
   taxon abs-abundance:  254270
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.5493"
   taxon abs-abundance:  122924
   taxon abs-abundance:  254112
  Processing taxon: "OTU.1208"
   taxon abs-abundance:  150106
  Processing taxon: "OTU.552"
   taxon abs-abundance:  111657
  Processing taxon: "OTU.1865"
   taxon abs-abundance:  1020695
  Processing taxon: "OTU.386"
   taxon abs-abundance:  383961
  Processing taxon: "OTU.7337"
  Processing taxon: "OTU.7353"
   taxon abs-abundance:  217629
   taxon abs-abundance:  191060
  Processing taxon: "OTU.1070"
  Processing taxon: "OTU.1105"
   taxon abs-abundance:  135231
   taxon abs-abundance:  103208
  Processing taxon: "OTU.7650"
   taxon abs-abundance:  680727
   WARNING: No bins for taxon; likely caused by no BD KDE
  Processing taxon: "OTU.218"
   taxon abs-abundance:  680195
  Processing taxon: "OTU.613"
   taxon abs-abundance:  122854
  Processing taxon: "OTU.973"
   taxon abs-abundance:  111582
  Processing taxon: "OTU.51"
   taxon abs-abundance:  508113
  Processing taxon: "OTU.5770"
   taxon abs-abundance:  169345
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   WARNING: No bins for taxon; likely caused by no BD KDE
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  Processing taxon: "OTU.3282"
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   WARNING: No bins for taxon; likely caused by no BD KDE
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