Accuracy as a function taxon abundance

Variable parameters:

Partition communities into 'dominant' and 'rare' subsets
- dominant/rare cutoff: 1% relative abundance?
Assess sensitivity & specificity for each subset
Note:
- Much less time to perform if using data from past simulation run datasets

Analysis:

Sup Figures:
- Same as above simulation runs, but split into 'dominant' vs 'rare'

User variables



In [2]:

    
workDir = '/home/nick/notebook/SIPSim/dev/bac_genome1210/'
sourceDir = os.path.join(workDir, 'atomIncorp_taxaIncorp')
buildDir = os.path.join(workDir, 'atomIncorp_taxaIncorp_abund')
R_dir = '/home/nick/notebook/SIPSim/lib/R/'

Init



In [3]:

    
import glob
from os.path import abspath
import nestly
from IPython.display import Image, display



In [4]:

    
%load_ext rpy2.ipython



In [5]:

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









    





Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Loading required package: grid



In [6]:

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

Nestly



In [71]:

    
# building tree structure
nest = nestly.Nest()

## varying params
#-- full run --#
nest.add('percIncorp', [0, 25, 50, 100])
nest.add('percTaxa', [1, 5, 10, 25, 50])
nest.add('rep', range(1,21))

## set params
nest.add('np', [6], create_dir=False)
nest.add('abs', ['1e9'], create_dir=False)
nest.add('subsample_mean', [30000], create_dir=False) 
nest.add('subsample_scale', [5000], create_dir=False) 
nest.add('BD_min', [1.71], create_dir=False)
nest.add('BD_max', [1.75], create_dir=False)
nest.add('padj', [0.1], create_dir=False)
nest.add('log2', [0.25], create_dir=False)
nest.add('topTaxaToPlot', [100], create_dir=False)

## input/output files
nest.add('buildDir', [buildDir], create_dir=False)
nest.add('sourceDir', [sourceDir], create_dir=False)
nest.add('frag_file', ['ampFrags_kde_dif'], create_dir=False)
nest.add('comm_file', ['comm.txt'], create_dir=False)
nest.add('R_dir', [R_dir], create_dir=False)

# building directory tree
nest.build(buildDir)



In [72]:

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



In [73]:

    
%%writefile $bashFile
#!/bin/bash

export PATH={R_dir}:$PATH

# copying DESeq files
cp {sourceDir}/{percIncorp}/{percTaxa}/{rep}/{comm_file} .
cp {sourceDir}/{percIncorp}/{percTaxa}/{rep}/OTU_n2_abs{abs}_sub-norm_DESeq2 .
cp {sourceDir}/{percIncorp}/{percTaxa}/{rep}/{frag_file}_incorp_BD-shift.txt .

## DESeq2
DESeq2_rare-dominant.r \
    OTU_n2_abs{abs}_sub-norm_DESeq2 \
    {comm_file} \
    -o OTU_n2_abs{abs}_sub-norm_DESeq2
    
## Confusion matrix
### dominant
DESeq2_confuseMtx.r \
    {frag_file}_incorp_BD-shift.txt \
    OTU_n2_abs{abs}_sub-norm_DESeq2_dom \
    --padj {padj} \
    -o DESeq2-cMtx_dom
### rare    
DESeq2_confuseMtx.r \
    {frag_file}_incorp_BD-shift.txt \
    OTU_n2_abs{abs}_sub-norm_DESeq2_rare \
    --padj {padj} \
    -o DESeq2-cMtx_rare









    



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



In [ ]:

    
!chmod 775 $bashFile



In [ ]:

    
!cd $workDir; \
    nestrun -j 10 --template-file $bashFile -d atomIncorp_taxaIncorp_abund --log-file log.txt









    



2015-08-06 20:22:53,344 * INFO * Template: ./SIPSimRun.sh
2015-08-06 20:22:53,362 * INFO * [82516] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/20
2015-08-06 20:22:53,385 * INFO * [82518] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/14
2015-08-06 20:22:53,400 * INFO * [82522] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/7
2015-08-06 20:22:53,410 * INFO * [82527] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/19
2015-08-06 20:22:53,419 * INFO * [82530] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/18
2015-08-06 20:22:53,433 * INFO * [82536] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/15
2015-08-06 20:22:53,451 * INFO * [82547] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/11
2015-08-06 20:22:53,473 * INFO * [82563] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/16
2015-08-06 20:22:53,497 * INFO * [82578] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/9
2015-08-06 20:22:53,521 * INFO * [82584] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/17
2015-08-06 20:23:46,258 * INFO * [82536] atomIncorp_taxaIncorp_abund/50/50/15 Finished with 0
2015-08-06 20:23:46,272 * INFO * [83027] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/8
2015-08-06 20:23:46,877 * INFO * [82527] atomIncorp_taxaIncorp_abund/50/50/19 Finished with 0
2015-08-06 20:23:46,890 * INFO * [83041] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/3
2015-08-06 20:24:01,624 * INFO * [82522] atomIncorp_taxaIncorp_abund/50/50/7 Finished with 0
2015-08-06 20:24:01,638 * INFO * [83179] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/13
2015-08-06 20:24:02,520 * INFO * [82518] atomIncorp_taxaIncorp_abund/50/50/14 Finished with 0
2015-08-06 20:24:02,533 * INFO * [83199] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/10
2015-08-06 20:24:06,578 * INFO * [82530] atomIncorp_taxaIncorp_abund/50/50/18 Finished with 0
2015-08-06 20:24:06,593 * INFO * [83211] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/2
2015-08-06 20:24:12,438 * INFO * [82516] atomIncorp_taxaIncorp_abund/50/50/20 Finished with 0
2015-08-06 20:24:12,449 * INFO * [83236] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/12
2015-08-06 20:24:12,627 * INFO * [82584] atomIncorp_taxaIncorp_abund/50/50/17 Finished with 0
2015-08-06 20:24:12,640 * INFO * [83248] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/1
2015-08-06 20:24:15,836 * INFO * [82578] atomIncorp_taxaIncorp_abund/50/50/9 Finished with 0
2015-08-06 20:24:15,850 * INFO * [83283] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/4
2015-08-06 20:24:21,068 * INFO * [82563] atomIncorp_taxaIncorp_abund/50/50/16 Finished with 0
2015-08-06 20:24:21,085 * INFO * [83317] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/5
2015-08-06 20:24:29,993 * INFO * [83179] atomIncorp_taxaIncorp_abund/50/50/13 Finished with 0
2015-08-06 20:24:30,002 * INFO * [83365] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/50/6
2015-08-06 20:24:31,474 * INFO * [82547] atomIncorp_taxaIncorp_abund/50/50/11 Finished with 0
2015-08-06 20:24:31,488 * INFO * [83377] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/20
2015-08-06 20:24:33,136 * INFO * [83211] atomIncorp_taxaIncorp_abund/50/50/2 Finished with 0
2015-08-06 20:24:33,149 * INFO * [83395] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/14
2015-08-06 20:24:43,393 * INFO * [83199] atomIncorp_taxaIncorp_abund/50/50/10 Finished with 0
2015-08-06 20:24:43,408 * INFO * [83456] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/7
2015-08-06 20:24:50,561 * INFO * [83236] atomIncorp_taxaIncorp_abund/50/50/12 Finished with 0
2015-08-06 20:24:50,576 * INFO * [83484] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/19
2015-08-06 20:24:58,062 * INFO * [83248] atomIncorp_taxaIncorp_abund/50/50/1 Finished with 0
2015-08-06 20:24:58,076 * INFO * [83502] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/18
2015-08-06 20:25:07,737 * INFO * [83027] atomIncorp_taxaIncorp_abund/50/50/8 Finished with 0
2015-08-06 20:25:07,748 * INFO * [83549] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/15
2015-08-06 20:25:11,165 * INFO * [83041] atomIncorp_taxaIncorp_abund/50/50/3 Finished with 0
2015-08-06 20:25:11,180 * INFO * [83591] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/11
2015-08-06 20:25:25,173 * INFO * [83365] atomIncorp_taxaIncorp_abund/50/50/6 Finished with 0
2015-08-06 20:25:25,188 * INFO * [83671] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/16
2015-08-06 20:25:25,696 * INFO * [83283] atomIncorp_taxaIncorp_abund/50/50/4 Finished with 0
2015-08-06 20:25:25,708 * INFO * [83683] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/9
2015-08-06 20:25:30,741 * INFO * [83317] atomIncorp_taxaIncorp_abund/50/50/5 Finished with 0
2015-08-06 20:25:30,750 * INFO * [83703] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/17
2015-08-06 20:25:36,323 * INFO * [83484] atomIncorp_taxaIncorp_abund/50/25/19 Finished with 0
2015-08-06 20:25:36,333 * INFO * [83745] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/8
2015-08-06 20:25:56,912 * INFO * [83456] atomIncorp_taxaIncorp_abund/50/25/7 Finished with 0
2015-08-06 20:25:56,919 * INFO * [83851] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/3
2015-08-06 20:25:57,840 * INFO * [83683] atomIncorp_taxaIncorp_abund/50/25/9 Finished with 0
2015-08-06 20:25:57,849 * INFO * [83863] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/13
2015-08-06 20:25:58,646 * INFO * [83591] atomIncorp_taxaIncorp_abund/50/25/11 Finished with 0
2015-08-06 20:25:58,658 * INFO * [83875] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/10
2015-08-06 20:25:59,448 * INFO * [83395] atomIncorp_taxaIncorp_abund/50/25/14 Finished with 0
2015-08-06 20:25:59,460 * INFO * [83887] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/2
2015-08-06 20:26:06,300 * INFO * [83377] atomIncorp_taxaIncorp_abund/50/25/20 Finished with 0
2015-08-06 20:26:06,312 * INFO * [83931] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/12
2015-08-06 20:26:09,461 * INFO * [83745] atomIncorp_taxaIncorp_abund/50/25/8 Finished with 0
2015-08-06 20:26:09,470 * INFO * [83951] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/1
2015-08-06 20:26:16,611 * INFO * [83703] atomIncorp_taxaIncorp_abund/50/25/17 Finished with 0
2015-08-06 20:26:16,621 * INFO * [83963] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/4
2015-08-06 20:26:18,121 * INFO * [83502] atomIncorp_taxaIncorp_abund/50/25/18 Finished with 0
2015-08-06 20:26:18,131 * INFO * [83981] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/5
2015-08-06 20:26:22,496 * INFO * [83671] atomIncorp_taxaIncorp_abund/50/25/16 Finished with 0
2015-08-06 20:26:22,504 * INFO * [84007] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/25/6
2015-08-06 20:26:23,195 * INFO * [83549] atomIncorp_taxaIncorp_abund/50/25/15 Finished with 0
2015-08-06 20:26:23,205 * INFO * [84019] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/20
2015-08-06 20:26:34,799 * INFO * [83863] atomIncorp_taxaIncorp_abund/50/25/13 Finished with 0
2015-08-06 20:26:34,813 * INFO * [84109] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/14
2015-08-06 20:26:47,946 * INFO * [83875] atomIncorp_taxaIncorp_abund/50/25/10 Finished with 0
2015-08-06 20:26:47,957 * INFO * [84159] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/7
2015-08-06 20:26:48,137 * INFO * [83981] atomIncorp_taxaIncorp_abund/50/25/5 Finished with 0
2015-08-06 20:26:48,147 * INFO * [84171] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/19
2015-08-06 20:26:55,843 * INFO * [83887] atomIncorp_taxaIncorp_abund/50/25/2 Finished with 0
2015-08-06 20:26:55,851 * INFO * [84221] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/18
2015-08-06 20:27:02,245 * INFO * [83851] atomIncorp_taxaIncorp_abund/50/25/3 Finished with 0
2015-08-06 20:27:02,257 * INFO * [84253] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/15
2015-08-06 20:27:02,555 * INFO * [83931] atomIncorp_taxaIncorp_abund/50/25/12 Finished with 0
2015-08-06 20:27:02,568 * INFO * [84265] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/11
2015-08-06 20:27:06,219 * INFO * [83963] atomIncorp_taxaIncorp_abund/50/25/4 Finished with 0
2015-08-06 20:27:06,227 * INFO * [84293] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/16
2015-08-06 20:27:19,854 * INFO * [84171] atomIncorp_taxaIncorp_abund/50/10/19 Finished with 0
2015-08-06 20:27:19,868 * INFO * [84355] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/9
2015-08-06 20:27:24,458 * INFO * [83951] atomIncorp_taxaIncorp_abund/50/25/1 Finished with 0
2015-08-06 20:27:24,471 * INFO * [84381] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/17
2015-08-06 20:27:35,162 * INFO * [84019] atomIncorp_taxaIncorp_abund/50/10/20 Finished with 0
2015-08-06 20:27:35,169 * INFO * [84415] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/8
2015-08-06 20:27:45,249 * INFO * [84253] atomIncorp_taxaIncorp_abund/50/10/15 Finished with 0
2015-08-06 20:27:45,262 * INFO * [84484] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/3
2015-08-06 20:28:03,223 * INFO * [84109] atomIncorp_taxaIncorp_abund/50/10/14 Finished with 0
2015-08-06 20:28:03,231 * INFO * [84555] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/13
2015-08-06 20:28:03,344 * INFO * [84221] atomIncorp_taxaIncorp_abund/50/10/18 Finished with 0
2015-08-06 20:28:03,357 * INFO * [84570] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/10
2015-08-06 20:28:04,851 * INFO * [84265] atomIncorp_taxaIncorp_abund/50/10/11 Finished with 0
2015-08-06 20:28:04,860 * INFO * [84583] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/2
2015-08-06 20:28:04,985 * INFO * [84007] atomIncorp_taxaIncorp_abund/50/25/6 Finished with 0
2015-08-06 20:28:05,000 * INFO * [84594] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/12
2015-08-06 20:28:32,969 * INFO * [84381] atomIncorp_taxaIncorp_abund/50/10/17 Finished with 0
2015-08-06 20:28:32,983 * INFO * [84660] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/1
2015-08-06 20:28:36,467 * INFO * [84355] atomIncorp_taxaIncorp_abund/50/10/9 Finished with 0
2015-08-06 20:28:36,483 * INFO * [84678] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/4
2015-08-06 20:28:38,788 * INFO * [84293] atomIncorp_taxaIncorp_abund/50/10/16 Finished with 0
2015-08-06 20:28:38,800 * INFO * [84698] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/5
2015-08-06 20:28:47,243 * INFO * [84159] atomIncorp_taxaIncorp_abund/50/10/7 Finished with 0
2015-08-06 20:28:47,260 * INFO * [84732] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/10/6
2015-08-06 20:28:50,496 * INFO * [84415] atomIncorp_taxaIncorp_abund/50/10/8 Finished with 0
2015-08-06 20:28:50,512 * INFO * [84750] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/20
2015-08-06 20:28:54,306 * INFO * [84484] atomIncorp_taxaIncorp_abund/50/10/3 Finished with 0
2015-08-06 20:28:54,324 * INFO * [84782] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/14
2015-08-06 20:29:04,359 * INFO * [84570] atomIncorp_taxaIncorp_abund/50/10/10 Finished with 0
2015-08-06 20:29:04,372 * INFO * [84832] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/7
2015-08-06 20:29:08,393 * INFO * [84583] atomIncorp_taxaIncorp_abund/50/10/2 Finished with 0
2015-08-06 20:29:08,412 * INFO * [84852] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/19
2015-08-06 20:29:12,678 * INFO * [84698] atomIncorp_taxaIncorp_abund/50/10/5 Finished with 0
2015-08-06 20:29:12,697 * INFO * [84872] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/18
2015-08-06 20:29:32,546 * INFO * [84594] atomIncorp_taxaIncorp_abund/50/10/12 Finished with 0
2015-08-06 20:29:32,558 * INFO * [84948] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/15
2015-08-06 20:29:44,625 * INFO * [84872] atomIncorp_taxaIncorp_abund/50/1/18 Finished with 0
2015-08-06 20:29:44,637 * INFO * [85004] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/11
2015-08-06 20:29:59,209 * INFO * [84555] atomIncorp_taxaIncorp_abund/50/10/13 Finished with 0
2015-08-06 20:29:59,223 * INFO * [85066] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/16
2015-08-06 20:30:00,340 * INFO * [84852] atomIncorp_taxaIncorp_abund/50/1/19 Finished with 0
2015-08-06 20:30:00,354 * INFO * [85078] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/9
2015-08-06 20:30:08,621 * INFO * [84660] atomIncorp_taxaIncorp_abund/50/10/1 Finished with 0
2015-08-06 20:30:08,636 * INFO * [85122] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/17
2015-08-06 20:30:09,016 * INFO * [84678] atomIncorp_taxaIncorp_abund/50/10/4 Finished with 0
2015-08-06 20:30:09,031 * INFO * [85134] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/8
2015-08-06 20:30:16,631 * INFO * [84750] atomIncorp_taxaIncorp_abund/50/1/20 Finished with 0
2015-08-06 20:30:16,649 * INFO * [85160] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/3
2015-08-06 20:30:18,988 * INFO * [84732] atomIncorp_taxaIncorp_abund/50/10/6 Finished with 0
2015-08-06 20:30:19,003 * INFO * [85172] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/13
2015-08-06 20:30:41,121 * INFO * [85078] atomIncorp_taxaIncorp_abund/50/1/9 Finished with 0
2015-08-06 20:30:41,134 * INFO * [85282] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/10
2015-08-06 20:30:45,030 * INFO * [85004] atomIncorp_taxaIncorp_abund/50/1/11 Finished with 0
2015-08-06 20:30:45,046 * INFO * [85308] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/2
2015-08-06 20:30:52,942 * INFO * [84948] atomIncorp_taxaIncorp_abund/50/1/15 Finished with 0
2015-08-06 20:30:52,957 * INFO * [85326] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/12
2015-08-06 20:30:58,782 * INFO * [84782] atomIncorp_taxaIncorp_abund/50/1/14 Finished with 0
2015-08-06 20:30:58,797 * INFO * [85354] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/1
2015-08-06 20:31:04,249 * INFO * [85134] atomIncorp_taxaIncorp_abund/50/1/8 Finished with 0
2015-08-06 20:31:04,262 * INFO * [85386] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/4
2015-08-06 20:31:12,058 * INFO * [85066] atomIncorp_taxaIncorp_abund/50/1/16 Finished with 0
2015-08-06 20:31:12,076 * INFO * [85420] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/5
2015-08-06 20:31:12,318 * INFO * [85122] atomIncorp_taxaIncorp_abund/50/1/17 Finished with 0
2015-08-06 20:31:12,337 * INFO * [85432] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/1/6
2015-08-06 20:31:13,227 * INFO * [84832] atomIncorp_taxaIncorp_abund/50/1/7 Finished with 0
2015-08-06 20:31:13,243 * INFO * [85444] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/20
2015-08-06 20:31:22,869 * INFO * [85326] atomIncorp_taxaIncorp_abund/50/1/12 Finished with 0
2015-08-06 20:31:22,882 * INFO * [85488] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/14
2015-08-06 20:31:33,313 * INFO * [85354] atomIncorp_taxaIncorp_abund/50/1/1 Finished with 0
2015-08-06 20:31:33,329 * INFO * [85536] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/7
2015-08-06 20:31:39,255 * INFO * [85160] atomIncorp_taxaIncorp_abund/50/1/3 Finished with 0
2015-08-06 20:31:39,268 * INFO * [85570] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/19
2015-08-06 20:31:40,372 * INFO * [85172] atomIncorp_taxaIncorp_abund/50/1/13 Finished with 0
2015-08-06 20:31:40,384 * INFO * [85582] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/18
2015-08-06 20:31:45,872 * INFO * [85432] atomIncorp_taxaIncorp_abund/50/1/6 Finished with 0
2015-08-06 20:31:45,887 * INFO * [85620] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/15
2015-08-06 20:31:52,309 * INFO * [85282] atomIncorp_taxaIncorp_abund/50/1/10 Finished with 0
2015-08-06 20:31:52,319 * INFO * [85648] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/11
2015-08-06 20:32:08,717 * INFO * [85488] atomIncorp_taxaIncorp_abund/50/5/14 Finished with 0
2015-08-06 20:32:08,729 * INFO * [85718] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/16
2015-08-06 20:32:09,561 * INFO * [85536] atomIncorp_taxaIncorp_abund/50/5/7 Finished with 0
2015-08-06 20:32:09,577 * INFO * [85736] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/9
2015-08-06 20:32:29,730 * INFO * [85386] atomIncorp_taxaIncorp_abund/50/1/4 Finished with 0
2015-08-06 20:32:29,742 * INFO * [85847] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/17
2015-08-06 20:32:31,774 * INFO * [85582] atomIncorp_taxaIncorp_abund/50/5/18 Finished with 0
2015-08-06 20:32:31,784 * INFO * [85867] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/8
2015-08-06 20:32:31,885 * INFO * [85570] atomIncorp_taxaIncorp_abund/50/5/19 Finished with 0
2015-08-06 20:32:31,893 * INFO * [85879] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/3
2015-08-06 20:32:35,935 * INFO * [85308] atomIncorp_taxaIncorp_abund/50/1/2 Finished with 0
2015-08-06 20:32:35,948 * INFO * [85907] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/13
2015-08-06 20:32:37,458 * INFO * [85420] atomIncorp_taxaIncorp_abund/50/1/5 Finished with 0
2015-08-06 20:32:37,470 * INFO * [85925] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/10
2015-08-06 20:32:38,356 * INFO * [85444] atomIncorp_taxaIncorp_abund/50/5/20 Finished with 0
2015-08-06 20:32:38,365 * INFO * [85937] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/2
2015-08-06 20:33:00,553 * INFO * [85847] atomIncorp_taxaIncorp_abund/50/5/17 Finished with 0
2015-08-06 20:33:00,562 * INFO * [86039] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/12
2015-08-06 20:33:01,518 * INFO * [85736] atomIncorp_taxaIncorp_abund/50/5/9 Finished with 0
2015-08-06 20:33:01,531 * INFO * [86051] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/1
2015-08-06 20:33:06,880 * INFO * [85718] atomIncorp_taxaIncorp_abund/50/5/16 Finished with 0
2015-08-06 20:33:06,891 * INFO * [86075] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/4
2015-08-06 20:33:07,403 * INFO * [85620] atomIncorp_taxaIncorp_abund/50/5/15 Finished with 0
2015-08-06 20:33:07,416 * INFO * [86087] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/5
2015-08-06 20:33:07,530 * INFO * [85907] atomIncorp_taxaIncorp_abund/50/5/13 Finished with 0
2015-08-06 20:33:07,543 * INFO * [86099] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/50/5/6
2015-08-06 20:33:09,020 * INFO * [85648] atomIncorp_taxaIncorp_abund/50/5/11 Finished with 0
2015-08-06 20:33:09,032 * INFO * [86111] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/20
2015-08-06 20:33:28,200 * INFO * [85925] atomIncorp_taxaIncorp_abund/50/5/10 Finished with 0
2015-08-06 20:33:28,213 * INFO * [86233] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/14
2015-08-06 20:33:33,809 * INFO * [86051] atomIncorp_taxaIncorp_abund/50/5/1 Finished with 0
2015-08-06 20:33:33,819 * INFO * [86261] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/7
2015-08-06 20:33:40,467 * INFO * [85879] atomIncorp_taxaIncorp_abund/50/5/3 Finished with 0
2015-08-06 20:33:40,480 * INFO * [86287] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/19
2015-08-06 20:33:48,398 * INFO * [86075] atomIncorp_taxaIncorp_abund/50/5/4 Finished with 0
2015-08-06 20:33:48,407 * INFO * [86319] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/18
2015-08-06 20:33:48,659 * INFO * [86039] atomIncorp_taxaIncorp_abund/50/5/12 Finished with 0
2015-08-06 20:33:48,669 * INFO * [86331] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/15
2015-08-06 20:33:52,562 * INFO * [85867] atomIncorp_taxaIncorp_abund/50/5/8 Finished with 0
2015-08-06 20:33:52,576 * INFO * [86351] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/11
2015-08-06 20:34:01,267 * INFO * [86111] atomIncorp_taxaIncorp_abund/0/50/20 Finished with 0
2015-08-06 20:34:01,279 * INFO * [86403] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/16
2015-08-06 20:34:03,053 * INFO * [85937] atomIncorp_taxaIncorp_abund/50/5/2 Finished with 0
2015-08-06 20:34:03,068 * INFO * [86423] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/9
2015-08-06 20:34:03,208 * INFO * [86261] atomIncorp_taxaIncorp_abund/0/50/7 Finished with 0
2015-08-06 20:34:03,219 * INFO * [86435] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/17
2015-08-06 20:34:24,471 * INFO * [86351] atomIncorp_taxaIncorp_abund/0/50/11 Finished with 0
2015-08-06 20:34:24,484 * INFO * [86552] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/8
2015-08-06 20:34:24,545 * INFO * [86331] atomIncorp_taxaIncorp_abund/0/50/15 Finished with 0
2015-08-06 20:34:24,560 * INFO * [86564] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/3
2015-08-06 20:34:28,247 * INFO * [86099] atomIncorp_taxaIncorp_abund/50/5/6 Finished with 0
2015-08-06 20:34:28,260 * INFO * [86608] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/13
2015-08-06 20:34:31,070 * INFO * [86087] atomIncorp_taxaIncorp_abund/50/5/5 Finished with 0
2015-08-06 20:34:31,081 * INFO * [86628] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/10
2015-08-06 20:34:34,888 * INFO * [86403] atomIncorp_taxaIncorp_abund/0/50/16 Finished with 0
2015-08-06 20:34:34,904 * INFO * [86656] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/2
2015-08-06 20:34:42,015 * INFO * [86319] atomIncorp_taxaIncorp_abund/0/50/18 Finished with 0
2015-08-06 20:34:42,033 * INFO * [86688] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/12
2015-08-06 20:34:50,897 * INFO * [86233] atomIncorp_taxaIncorp_abund/0/50/14 Finished with 0
2015-08-06 20:34:50,908 * INFO * [86724] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/1
2015-08-06 20:34:55,029 * INFO * [86564] atomIncorp_taxaIncorp_abund/0/50/3 Finished with 0
2015-08-06 20:34:55,042 * INFO * [86760] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/4
2015-08-06 20:34:59,038 * INFO * [86608] atomIncorp_taxaIncorp_abund/0/50/13 Finished with 0
2015-08-06 20:34:59,052 * INFO * [86780] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/5
2015-08-06 20:35:02,185 * INFO * [86423] atomIncorp_taxaIncorp_abund/0/50/9 Finished with 0
2015-08-06 20:35:02,197 * INFO * [86807] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/50/6
2015-08-06 20:35:17,101 * INFO * [86435] atomIncorp_taxaIncorp_abund/0/50/17 Finished with 0
2015-08-06 20:35:17,117 * INFO * [86891] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/20
2015-08-06 20:35:20,126 * INFO * [86724] atomIncorp_taxaIncorp_abund/0/50/1 Finished with 0
2015-08-06 20:35:20,144 * INFO * [86911] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/14
2015-08-06 20:35:26,169 * INFO * [86287] atomIncorp_taxaIncorp_abund/0/50/19 Finished with 0
2015-08-06 20:35:26,184 * INFO * [86953] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/7
2015-08-06 20:35:32,893 * INFO * [86656] atomIncorp_taxaIncorp_abund/0/50/2 Finished with 0
2015-08-06 20:35:32,908 * INFO * [86985] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/19
2015-08-06 20:35:45,711 * INFO * [86780] atomIncorp_taxaIncorp_abund/0/50/5 Finished with 0
2015-08-06 20:35:45,728 * INFO * [87027] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/18
2015-08-06 20:35:49,023 * INFO * [86628] atomIncorp_taxaIncorp_abund/0/50/10 Finished with 0
2015-08-06 20:35:49,041 * INFO * [87055] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/15
2015-08-06 20:35:49,124 * INFO * [86760] atomIncorp_taxaIncorp_abund/0/50/4 Finished with 0
2015-08-06 20:35:49,137 * INFO * [87065] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/11
2015-08-06 20:35:53,299 * INFO * [86552] atomIncorp_taxaIncorp_abund/0/50/8 Finished with 0
2015-08-06 20:35:53,312 * INFO * [87093] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/16
2015-08-06 20:36:09,855 * INFO * [86891] atomIncorp_taxaIncorp_abund/0/25/20 Finished with 0
2015-08-06 20:36:09,863 * INFO * [87187] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/9
2015-08-06 20:36:11,410 * INFO * [86911] atomIncorp_taxaIncorp_abund/0/25/14 Finished with 0
2015-08-06 20:36:11,421 * INFO * [87199] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/17
2015-08-06 20:36:17,719 * INFO * [86688] atomIncorp_taxaIncorp_abund/0/50/12 Finished with 0
2015-08-06 20:36:17,731 * INFO * [87223] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/8
2015-08-06 20:36:17,749 * INFO * [86985] atomIncorp_taxaIncorp_abund/0/25/19 Finished with 0
2015-08-06 20:36:17,759 * INFO * [87229] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/3
2015-08-06 20:36:23,983 * INFO * [87027] atomIncorp_taxaIncorp_abund/0/25/18 Finished with 0
2015-08-06 20:36:23,991 * INFO * [87277] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/13
2015-08-06 20:36:24,239 * INFO * [87093] atomIncorp_taxaIncorp_abund/0/25/16 Finished with 0
2015-08-06 20:36:24,247 * INFO * [87289] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/10
2015-08-06 20:36:32,106 * INFO * [86807] atomIncorp_taxaIncorp_abund/0/50/6 Finished with 0
2015-08-06 20:36:32,118 * INFO * [87351] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/2
2015-08-06 20:36:47,296 * INFO * [86953] atomIncorp_taxaIncorp_abund/0/25/7 Finished with 0
2015-08-06 20:36:47,304 * INFO * [87423] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/12
2015-08-06 20:36:48,932 * INFO * [87223] atomIncorp_taxaIncorp_abund/0/25/8 Finished with 0
2015-08-06 20:36:48,943 * INFO * [87435] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/1
2015-08-06 20:36:50,275 * INFO * [87187] atomIncorp_taxaIncorp_abund/0/25/9 Finished with 0
2015-08-06 20:36:50,288 * INFO * [87447] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/4
2015-08-06 20:36:59,518 * INFO * [87055] atomIncorp_taxaIncorp_abund/0/25/15 Finished with 0
2015-08-06 20:36:59,528 * INFO * [87495] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/5
2015-08-06 20:37:04,180 * INFO * [87199] atomIncorp_taxaIncorp_abund/0/25/17 Finished with 0
2015-08-06 20:37:04,193 * INFO * [87531] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/25/6
2015-08-06 20:37:20,295 * INFO * [87423] atomIncorp_taxaIncorp_abund/0/25/12 Finished with 0
2015-08-06 20:37:20,308 * INFO * [87611] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/20
2015-08-06 20:37:21,201 * INFO * [87435] atomIncorp_taxaIncorp_abund/0/25/1 Finished with 0
2015-08-06 20:37:21,216 * INFO * [87623] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/14
2015-08-06 20:37:21,682 * INFO * [87229] atomIncorp_taxaIncorp_abund/0/25/3 Finished with 0
2015-08-06 20:37:21,695 * INFO * [87636] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/7
2015-08-06 20:37:24,740 * INFO * [87277] atomIncorp_taxaIncorp_abund/0/25/13 Finished with 0
2015-08-06 20:37:24,751 * INFO * [87653] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/19
2015-08-06 20:37:27,846 * INFO * [87351] atomIncorp_taxaIncorp_abund/0/25/2 Finished with 0
2015-08-06 20:37:27,858 * INFO * [87665] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/18
2015-08-06 20:37:29,586 * INFO * [87065] atomIncorp_taxaIncorp_abund/0/25/11 Finished with 0
2015-08-06 20:37:29,601 * INFO * [87677] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/15
2015-08-06 20:37:31,220 * INFO * [87289] atomIncorp_taxaIncorp_abund/0/25/10 Finished with 0
2015-08-06 20:37:31,237 * INFO * [87689] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/11
2015-08-06 20:37:52,074 * INFO * [87531] atomIncorp_taxaIncorp_abund/0/25/6 Finished with 0
2015-08-06 20:37:52,089 * INFO * [87821] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/16
2015-08-06 20:37:52,646 * INFO * [87611] atomIncorp_taxaIncorp_abund/0/10/20 Finished with 0
2015-08-06 20:37:52,660 * INFO * [87833] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/9
2015-08-06 20:37:58,278 * INFO * [87677] atomIncorp_taxaIncorp_abund/0/10/15 Finished with 0
2015-08-06 20:37:58,292 * INFO * [87853] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/17
2015-08-06 20:38:00,799 * INFO * [87495] atomIncorp_taxaIncorp_abund/0/25/5 Finished with 0
2015-08-06 20:38:00,809 * INFO * [87871] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/8
2015-08-06 20:38:05,089 * INFO * [87447] atomIncorp_taxaIncorp_abund/0/25/4 Finished with 0
2015-08-06 20:38:05,102 * INFO * [87909] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/3
2015-08-06 20:38:12,980 * INFO * [87636] atomIncorp_taxaIncorp_abund/0/10/7 Finished with 0
2015-08-06 20:38:12,996 * INFO * [87959] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/13
2015-08-06 20:38:29,664 * INFO * [87623] atomIncorp_taxaIncorp_abund/0/10/14 Finished with 0
2015-08-06 20:38:29,676 * INFO * [88065] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/10
2015-08-06 20:38:34,897 * INFO * [87689] atomIncorp_taxaIncorp_abund/0/10/11 Finished with 0
2015-08-06 20:38:34,910 * INFO * [88095] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/2
2015-08-06 20:38:35,864 * INFO * [87909] atomIncorp_taxaIncorp_abund/0/10/3 Finished with 0
2015-08-06 20:38:35,880 * INFO * [88115] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/12
2015-08-06 20:38:40,407 * INFO * [87821] atomIncorp_taxaIncorp_abund/0/10/16 Finished with 0
2015-08-06 20:38:40,419 * INFO * [88143] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/1
2015-08-06 20:38:43,999 * INFO * [87871] atomIncorp_taxaIncorp_abund/0/10/8 Finished with 0
2015-08-06 20:38:44,010 * INFO * [88155] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/4
2015-08-06 20:38:44,893 * INFO * [87959] atomIncorp_taxaIncorp_abund/0/10/13 Finished with 0
2015-08-06 20:38:44,904 * INFO * [88167] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/5
2015-08-06 20:38:45,134 * INFO * [87653] atomIncorp_taxaIncorp_abund/0/10/19 Finished with 0
2015-08-06 20:38:45,146 * INFO * [88179] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/10/6
2015-08-06 20:38:50,947 * INFO * [87665] atomIncorp_taxaIncorp_abund/0/10/18 Finished with 0
2015-08-06 20:38:50,955 * INFO * [88197] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/20
2015-08-06 20:38:57,296 * INFO * [87833] atomIncorp_taxaIncorp_abund/0/10/9 Finished with 0
2015-08-06 20:38:57,307 * INFO * [88235] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/14
2015-08-06 20:39:05,152 * INFO * [87853] atomIncorp_taxaIncorp_abund/0/10/17 Finished with 0
2015-08-06 20:39:05,165 * INFO * [88291] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/7
2015-08-06 20:39:19,032 * INFO * [88197] atomIncorp_taxaIncorp_abund/0/1/20 Finished with 0
2015-08-06 20:39:19,047 * INFO * [88361] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/19
2015-08-06 20:39:27,314 * INFO * [88143] atomIncorp_taxaIncorp_abund/0/10/1 Finished with 0
2015-08-06 20:39:27,328 * INFO * [88419] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/18
2015-08-06 20:39:33,231 * INFO * [88155] atomIncorp_taxaIncorp_abund/0/10/4 Finished with 0
2015-08-06 20:39:33,248 * INFO * [88469] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/15
2015-08-06 20:39:33,649 * INFO * [88291] atomIncorp_taxaIncorp_abund/0/1/7 Finished with 0
2015-08-06 20:39:33,661 * INFO * [88481] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/11
2015-08-06 20:39:34,572 * INFO * [88065] atomIncorp_taxaIncorp_abund/0/10/10 Finished with 0
2015-08-06 20:39:34,583 * INFO * [88495] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/16
2015-08-06 20:39:35,144 * INFO * [88095] atomIncorp_taxaIncorp_abund/0/10/2 Finished with 0
2015-08-06 20:39:35,160 * INFO * [88513] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/9
2015-08-06 20:39:37,231 * INFO * [88115] atomIncorp_taxaIncorp_abund/0/10/12 Finished with 0
2015-08-06 20:39:37,244 * INFO * [88525] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/17
2015-08-06 20:39:48,034 * INFO * [88179] atomIncorp_taxaIncorp_abund/0/10/6 Finished with 0
2015-08-06 20:39:48,043 * INFO * [88559] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/8
2015-08-06 20:39:55,460 * INFO * [88167] atomIncorp_taxaIncorp_abund/0/10/5 Finished with 0
2015-08-06 20:39:55,471 * INFO * [88613] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/3
2015-08-06 20:40:04,190 * INFO * [88469] atomIncorp_taxaIncorp_abund/0/1/15 Finished with 0
2015-08-06 20:40:04,199 * INFO * [88675] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/13
2015-08-06 20:40:04,491 * INFO * [88361] atomIncorp_taxaIncorp_abund/0/1/19 Finished with 0
2015-08-06 20:40:04,503 * INFO * [88687] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/10
2015-08-06 20:40:17,365 * INFO * [88559] atomIncorp_taxaIncorp_abund/0/1/8 Finished with 0
2015-08-06 20:40:17,375 * INFO * [88789] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/2
2015-08-06 20:40:18,807 * INFO * [88513] atomIncorp_taxaIncorp_abund/0/1/9 Finished with 0
2015-08-06 20:40:18,821 * INFO * [88801] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/12
2015-08-06 20:40:19,332 * INFO * [88235] atomIncorp_taxaIncorp_abund/0/1/14 Finished with 0
2015-08-06 20:40:19,343 * INFO * [88817] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/1
2015-08-06 20:40:27,965 * INFO * [88419] atomIncorp_taxaIncorp_abund/0/1/18 Finished with 0
2015-08-06 20:40:27,974 * INFO * [88863] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/4
2015-08-06 20:40:28,889 * INFO * [88481] atomIncorp_taxaIncorp_abund/0/1/11 Finished with 0
2015-08-06 20:40:28,899 * INFO * [88875] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/5
2015-08-06 20:40:33,858 * INFO * [88525] atomIncorp_taxaIncorp_abund/0/1/17 Finished with 0
2015-08-06 20:40:33,864 * INFO * [88903] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/1/6
2015-08-06 20:40:39,158 * INFO * [88495] atomIncorp_taxaIncorp_abund/0/1/16 Finished with 0
2015-08-06 20:40:39,165 * INFO * [88941] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/20
2015-08-06 20:40:39,773 * INFO * [88613] atomIncorp_taxaIncorp_abund/0/1/3 Finished with 0
2015-08-06 20:40:39,783 * INFO * [88961] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/14
2015-08-06 20:40:47,303 * INFO * [88687] atomIncorp_taxaIncorp_abund/0/1/10 Finished with 0
2015-08-06 20:40:47,315 * INFO * [88989] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/7
2015-08-06 20:40:55,483 * INFO * [88863] atomIncorp_taxaIncorp_abund/0/1/4 Finished with 0
2015-08-06 20:40:55,493 * INFO * [89053] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/19
2015-08-06 20:40:56,730 * INFO * [88675] atomIncorp_taxaIncorp_abund/0/1/13 Finished with 0
2015-08-06 20:40:56,737 * INFO * [89065] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/18
2015-08-06 20:40:56,864 * INFO * [88789] atomIncorp_taxaIncorp_abund/0/1/2 Finished with 0
2015-08-06 20:40:56,875 * INFO * [89077] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/15
2015-08-06 20:41:02,812 * INFO * [88817] atomIncorp_taxaIncorp_abund/0/1/1 Finished with 0
2015-08-06 20:41:02,820 * INFO * [89123] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/11
2015-08-06 20:41:08,871 * INFO * [88941] atomIncorp_taxaIncorp_abund/0/5/20 Finished with 0
2015-08-06 20:41:08,880 * INFO * [89163] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/16
2015-08-06 20:41:27,080 * INFO * [88801] atomIncorp_taxaIncorp_abund/0/1/12 Finished with 0
2015-08-06 20:41:27,092 * INFO * [89273] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/9
2015-08-06 20:41:29,569 * INFO * [89053] atomIncorp_taxaIncorp_abund/0/5/19 Finished with 0
2015-08-06 20:41:29,581 * INFO * [89285] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/17
2015-08-06 20:41:37,079 * INFO * [88903] atomIncorp_taxaIncorp_abund/0/1/6 Finished with 0
2015-08-06 20:41:37,093 * INFO * [89319] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/8
2015-08-06 20:41:37,912 * INFO * [89123] atomIncorp_taxaIncorp_abund/0/5/11 Finished with 0
2015-08-06 20:41:37,927 * INFO * [89331] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/3
2015-08-06 20:41:42,454 * INFO * [88875] atomIncorp_taxaIncorp_abund/0/1/5 Finished with 0
2015-08-06 20:41:42,467 * INFO * [89365] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/13
2015-08-06 20:41:42,916 * INFO * [88961] atomIncorp_taxaIncorp_abund/0/5/14 Finished with 0
2015-08-06 20:41:42,925 * INFO * [89377] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/10
2015-08-06 20:41:46,065 * INFO * [89077] atomIncorp_taxaIncorp_abund/0/5/15 Finished with 0
2015-08-06 20:41:46,077 * INFO * [89397] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/2
2015-08-06 20:41:57,496 * INFO * [89273] atomIncorp_taxaIncorp_abund/0/5/9 Finished with 0
2015-08-06 20:41:57,509 * INFO * [89467] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/12
2015-08-06 20:42:10,857 * INFO * [89163] atomIncorp_taxaIncorp_abund/0/5/16 Finished with 0
2015-08-06 20:42:10,872 * INFO * [89533] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/1
2015-08-06 20:42:10,874 * INFO * [88989] atomIncorp_taxaIncorp_abund/0/5/7 Finished with 0
2015-08-06 20:42:10,883 * INFO * [89535] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/4
2015-08-06 20:42:12,581 * INFO * [89397] atomIncorp_taxaIncorp_abund/0/5/2 Finished with 0
2015-08-06 20:42:12,593 * INFO * [89555] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/5
2015-08-06 20:42:12,903 * INFO * [89065] atomIncorp_taxaIncorp_abund/0/5/18 Finished with 0
2015-08-06 20:42:12,915 * INFO * [89567] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/0/5/6
2015-08-06 20:42:24,297 * INFO * [89467] atomIncorp_taxaIncorp_abund/0/5/12 Finished with 0
2015-08-06 20:42:24,308 * INFO * [89627] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/20
2015-08-06 20:42:28,835 * INFO * [89377] atomIncorp_taxaIncorp_abund/0/5/10 Finished with 0
2015-08-06 20:42:28,848 * INFO * [89661] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/14
2015-08-06 20:42:32,853 * INFO * [89331] atomIncorp_taxaIncorp_abund/0/5/3 Finished with 0
2015-08-06 20:42:32,866 * INFO * [89697] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/7
2015-08-06 20:42:44,071 * INFO * [89319] atomIncorp_taxaIncorp_abund/0/5/8 Finished with 0
2015-08-06 20:42:44,076 * INFO * [89845] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/19
2015-08-06 20:42:50,306 * INFO * [89533] atomIncorp_taxaIncorp_abund/0/5/1 Finished with 0
2015-08-06 20:42:50,317 * INFO * [89952] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/18
2015-08-06 20:42:52,106 * INFO * [89627] atomIncorp_taxaIncorp_abund/100/50/20 Finished with 0
2015-08-06 20:42:52,112 * INFO * [89986] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/15
2015-08-06 20:42:52,154 * INFO * [89661] atomIncorp_taxaIncorp_abund/100/50/14 Finished with 0
2015-08-06 20:42:52,159 * INFO * [89998] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/11
2015-08-06 20:42:54,067 * INFO * [89555] atomIncorp_taxaIncorp_abund/0/5/5 Finished with 0
2015-08-06 20:42:54,073 * INFO * [90018] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/16
2015-08-06 20:42:57,134 * INFO * [89697] atomIncorp_taxaIncorp_abund/100/50/7 Finished with 0
2015-08-06 20:42:57,139 * INFO * [90044] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/9
2015-08-06 20:42:57,577 * INFO * [89365] atomIncorp_taxaIncorp_abund/0/5/13 Finished with 0
2015-08-06 20:42:57,583 * INFO * [90056] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/17
2015-08-06 20:42:59,458 * INFO * [89567] atomIncorp_taxaIncorp_abund/0/5/6 Finished with 0
2015-08-06 20:42:59,463 * INFO * [90082] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/8
2015-08-06 20:43:00,586 * INFO * [89285] atomIncorp_taxaIncorp_abund/0/5/17 Finished with 0
2015-08-06 20:43:00,591 * INFO * [90108] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/3
2015-08-06 20:43:09,272 * INFO * [89952] atomIncorp_taxaIncorp_abund/100/50/18 Finished with 0
2015-08-06 20:43:09,278 * INFO * [90188] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/13
2015-08-06 20:43:12,325 * INFO * [89998] atomIncorp_taxaIncorp_abund/100/50/11 Finished with 0
2015-08-06 20:43:12,330 * INFO * [90232] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/10
2015-08-06 20:43:14,844 * INFO * [89986] atomIncorp_taxaIncorp_abund/100/50/15 Finished with 0
2015-08-06 20:43:14,851 * INFO * [90250] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/2
2015-08-06 20:43:18,715 * INFO * [90044] atomIncorp_taxaIncorp_abund/100/50/9 Finished with 0
2015-08-06 20:43:18,721 * INFO * [90278] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/12
2015-08-06 20:43:19,459 * INFO * [90056] atomIncorp_taxaIncorp_abund/100/50/17 Finished with 0
2015-08-06 20:43:19,470 * INFO * [90292] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/1
2015-08-06 20:43:30,126 * INFO * [89535] atomIncorp_taxaIncorp_abund/0/5/4 Finished with 0
2015-08-06 20:43:30,134 * INFO * [90362] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/4
2015-08-06 20:43:31,596 * INFO * [89845] atomIncorp_taxaIncorp_abund/100/50/19 Finished with 0
2015-08-06 20:43:31,604 * INFO * [90374] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/5
2015-08-06 20:43:39,235 * INFO * [90018] atomIncorp_taxaIncorp_abund/100/50/16 Finished with 0
2015-08-06 20:43:39,244 * INFO * [90434] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/50/6
2015-08-06 20:43:40,580 * INFO * [90082] atomIncorp_taxaIncorp_abund/100/50/8 Finished with 0
2015-08-06 20:43:40,590 * INFO * [90452] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/20
2015-08-06 20:43:48,519 * INFO * [90278] atomIncorp_taxaIncorp_abund/100/50/12 Finished with 0
2015-08-06 20:43:48,528 * INFO * [90480] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/14
2015-08-06 20:43:53,882 * INFO * [90292] atomIncorp_taxaIncorp_abund/100/50/1 Finished with 0
2015-08-06 20:43:53,889 * INFO * [90526] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/7
2015-08-06 20:43:58,124 * INFO * [90108] atomIncorp_taxaIncorp_abund/100/50/3 Finished with 0
2015-08-06 20:43:58,131 * INFO * [90546] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/19
2015-08-06 20:43:58,237 * INFO * [90188] atomIncorp_taxaIncorp_abund/100/50/13 Finished with 0
2015-08-06 20:43:58,245 * INFO * [90558] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/18
2015-08-06 20:43:58,954 * INFO * [90232] atomIncorp_taxaIncorp_abund/100/50/10 Finished with 0
2015-08-06 20:43:58,961 * INFO * [90570] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/15
2015-08-06 20:44:13,601 * INFO * [90362] atomIncorp_taxaIncorp_abund/100/50/4 Finished with 0
2015-08-06 20:44:13,609 * INFO * [90686] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/11
2015-08-06 20:44:15,523 * INFO * [90434] atomIncorp_taxaIncorp_abund/100/50/6 Finished with 0
2015-08-06 20:44:15,528 * INFO * [90698] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/16
2015-08-06 20:44:18,697 * INFO * [90452] atomIncorp_taxaIncorp_abund/100/25/20 Finished with 0
2015-08-06 20:44:18,705 * INFO * [90740] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/9
2015-08-06 20:44:19,098 * INFO * [90250] atomIncorp_taxaIncorp_abund/100/50/2 Finished with 0
2015-08-06 20:44:19,103 * INFO * [90752] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/17
2015-08-06 20:44:24,226 * INFO * [90546] atomIncorp_taxaIncorp_abund/100/25/19 Finished with 0
2015-08-06 20:44:24,231 * INFO * [90770] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/8
2015-08-06 20:44:25,703 * INFO * [90480] atomIncorp_taxaIncorp_abund/100/25/14 Finished with 0
2015-08-06 20:44:25,711 * INFO * [90796] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/3
2015-08-06 20:44:33,469 * INFO * [90374] atomIncorp_taxaIncorp_abund/100/50/5 Finished with 0
2015-08-06 20:44:33,476 * INFO * [90874] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/13
2015-08-06 20:44:36,698 * INFO * [90526] atomIncorp_taxaIncorp_abund/100/25/7 Finished with 0
2015-08-06 20:44:36,702 * INFO * [90922] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/10
2015-08-06 20:44:36,754 * INFO * [90570] atomIncorp_taxaIncorp_abund/100/25/15 Finished with 0
2015-08-06 20:44:36,758 * INFO * [90934] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/2
2015-08-06 20:44:41,470 * INFO * [90740] atomIncorp_taxaIncorp_abund/100/25/9 Finished with 0
2015-08-06 20:44:41,477 * INFO * [90985] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/12
2015-08-06 20:44:44,177 * INFO * [90752] atomIncorp_taxaIncorp_abund/100/25/17 Finished with 0
2015-08-06 20:44:44,184 * INFO * [91007] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/1
2015-08-06 20:44:50,362 * INFO * [90558] atomIncorp_taxaIncorp_abund/100/25/18 Finished with 0
2015-08-06 20:44:50,367 * INFO * [91096] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/4
2015-08-06 20:44:52,538 * INFO * [90796] atomIncorp_taxaIncorp_abund/100/25/3 Finished with 0
2015-08-06 20:44:52,543 * INFO * [91120] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/5
2015-08-06 20:44:54,732 * INFO * [90770] atomIncorp_taxaIncorp_abund/100/25/8 Finished with 0
2015-08-06 20:44:54,738 * INFO * [91154] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/25/6
2015-08-06 20:45:06,756 * INFO * [90686] atomIncorp_taxaIncorp_abund/100/25/11 Finished with 0
2015-08-06 20:45:06,763 * INFO * [91252] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/20
2015-08-06 20:45:07,319 * INFO * [90698] atomIncorp_taxaIncorp_abund/100/25/16 Finished with 0
2015-08-06 20:45:07,330 * INFO * [91264] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/14
2015-08-06 20:45:09,548 * INFO * [90985] atomIncorp_taxaIncorp_abund/100/25/12 Finished with 0
2015-08-06 20:45:09,558 * INFO * [91276] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/7
2015-08-06 20:45:10,445 * INFO * [90922] atomIncorp_taxaIncorp_abund/100/25/10 Finished with 0
2015-08-06 20:45:10,451 * INFO * [91288] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/19
2015-08-06 20:45:12,320 * INFO * [91007] atomIncorp_taxaIncorp_abund/100/25/1 Finished with 0
2015-08-06 20:45:12,330 * INFO * [91306] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/18
2015-08-06 20:45:19,262 * INFO * [91096] atomIncorp_taxaIncorp_abund/100/25/4 Finished with 0
2015-08-06 20:45:19,269 * INFO * [91356] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/15
2015-08-06 20:45:24,877 * INFO * [90934] atomIncorp_taxaIncorp_abund/100/25/2 Finished with 0
2015-08-06 20:45:24,884 * INFO * [91406] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/11
2015-08-06 20:45:30,690 * INFO * [90874] atomIncorp_taxaIncorp_abund/100/25/13 Finished with 0
2015-08-06 20:45:30,698 * INFO * [91453] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/16
2015-08-06 20:45:36,941 * INFO * [91120] atomIncorp_taxaIncorp_abund/100/25/5 Finished with 0
2015-08-06 20:45:36,946 * INFO * [91519] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/9
2015-08-06 20:45:37,770 * INFO * [91154] atomIncorp_taxaIncorp_abund/100/25/6 Finished with 0
2015-08-06 20:45:37,775 * INFO * [91539] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/17
2015-08-06 20:45:41,240 * INFO * [91306] atomIncorp_taxaIncorp_abund/100/10/18 Finished with 0
2015-08-06 20:45:41,248 * INFO * [91559] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/8
2015-08-06 20:45:43,744 * INFO * [91356] atomIncorp_taxaIncorp_abund/100/10/15 Finished with 0
2015-08-06 20:45:43,752 * INFO * [91577] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/3
2015-08-06 20:45:52,140 * INFO * [91406] atomIncorp_taxaIncorp_abund/100/10/11 Finished with 0
2015-08-06 20:45:52,152 * INFO * [91619] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/13
2015-08-06 20:45:53,588 * INFO * [91264] atomIncorp_taxaIncorp_abund/100/10/14 Finished with 0
2015-08-06 20:45:53,595 * INFO * [91651] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/10
2015-08-06 20:45:57,029 * INFO * [91276] atomIncorp_taxaIncorp_abund/100/10/7 Finished with 0
2015-08-06 20:45:57,035 * INFO * [91679] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/2
2015-08-06 20:45:59,785 * INFO * [91252] atomIncorp_taxaIncorp_abund/100/10/20 Finished with 0
2015-08-06 20:45:59,793 * INFO * [91705] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/12
2015-08-06 20:46:08,403 * INFO * [91288] atomIncorp_taxaIncorp_abund/100/10/19 Finished with 0
2015-08-06 20:46:08,408 * INFO * [91755] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/1
2015-08-06 20:46:09,326 * INFO * [91453] atomIncorp_taxaIncorp_abund/100/10/16 Finished with 0
2015-08-06 20:46:09,333 * INFO * [91773] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/4
2015-08-06 20:46:12,877 * INFO * [91539] atomIncorp_taxaIncorp_abund/100/10/17 Finished with 0
2015-08-06 20:46:12,883 * INFO * [91812] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/5
2015-08-06 20:46:20,228 * INFO * [91619] atomIncorp_taxaIncorp_abund/100/10/13 Finished with 0
2015-08-06 20:46:20,235 * INFO * [91889] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/10/6
2015-08-06 20:46:20,313 * INFO * [91577] atomIncorp_taxaIncorp_abund/100/10/3 Finished with 0
2015-08-06 20:46:20,321 * INFO * [91901] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/20
2015-08-06 20:46:23,530 * INFO * [91519] atomIncorp_taxaIncorp_abund/100/10/9 Finished with 0
2015-08-06 20:46:23,536 * INFO * [91929] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/14
2015-08-06 20:46:27,210 * INFO * [91559] atomIncorp_taxaIncorp_abund/100/10/8 Finished with 0
2015-08-06 20:46:27,217 * INFO * [91971] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/7
2015-08-06 20:46:33,795 * INFO * [91705] atomIncorp_taxaIncorp_abund/100/10/12 Finished with 0
2015-08-06 20:46:33,803 * INFO * [92035] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/19
2015-08-06 20:46:38,741 * INFO * [91812] atomIncorp_taxaIncorp_abund/100/10/5 Finished with 0
2015-08-06 20:46:38,754 * INFO * [92065] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/18
2015-08-06 20:46:39,725 * INFO * [91651] atomIncorp_taxaIncorp_abund/100/10/10 Finished with 0
2015-08-06 20:46:39,739 * INFO * [92083] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/15
2015-08-06 20:46:40,473 * INFO * [91773] atomIncorp_taxaIncorp_abund/100/10/4 Finished with 0
2015-08-06 20:46:40,482 * INFO * [92098] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/11
2015-08-06 20:46:47,996 * INFO * [91679] atomIncorp_taxaIncorp_abund/100/10/2 Finished with 0
2015-08-06 20:46:48,007 * INFO * [92143] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/16
2015-08-06 20:46:52,846 * INFO * [91755] atomIncorp_taxaIncorp_abund/100/10/1 Finished with 0
2015-08-06 20:46:52,859 * INFO * [92177] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/9
2015-08-06 20:46:53,923 * INFO * [91929] atomIncorp_taxaIncorp_abund/100/1/14 Finished with 0
2015-08-06 20:46:53,935 * INFO * [92197] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/17
2015-08-06 20:46:56,154 * INFO * [91889] atomIncorp_taxaIncorp_abund/100/10/6 Finished with 0
2015-08-06 20:46:56,166 * INFO * [92227] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/8
2015-08-06 20:47:06,134 * INFO * [91901] atomIncorp_taxaIncorp_abund/100/1/20 Finished with 0
2015-08-06 20:47:06,143 * INFO * [92286] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/3
2015-08-06 20:47:09,868 * INFO * [92065] atomIncorp_taxaIncorp_abund/100/1/18 Finished with 0
2015-08-06 20:47:09,879 * INFO * [92332] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/13
2015-08-06 20:47:19,876 * INFO * [92035] atomIncorp_taxaIncorp_abund/100/1/19 Finished with 0
2015-08-06 20:47:19,884 * INFO * [92406] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/10
2015-08-06 20:47:23,473 * INFO * [91971] atomIncorp_taxaIncorp_abund/100/1/7 Finished with 0
2015-08-06 20:47:23,484 * INFO * [92434] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/2
2015-08-06 20:47:24,930 * INFO * [92098] atomIncorp_taxaIncorp_abund/100/1/11 Finished with 0
2015-08-06 20:47:24,944 * INFO * [92446] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/12
2015-08-06 20:47:31,571 * INFO * [92177] atomIncorp_taxaIncorp_abund/100/1/9 Finished with 0
2015-08-06 20:47:31,578 * INFO * [92488] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/1
2015-08-06 20:47:33,363 * INFO * [92227] atomIncorp_taxaIncorp_abund/100/1/8 Finished with 0
2015-08-06 20:47:33,375 * INFO * [92500] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/4
2015-08-06 20:47:33,888 * INFO * [92083] atomIncorp_taxaIncorp_abund/100/1/15 Finished with 0
2015-08-06 20:47:33,899 * INFO * [92512] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/5
2015-08-06 20:47:39,009 * INFO * [92143] atomIncorp_taxaIncorp_abund/100/1/16 Finished with 0
2015-08-06 20:47:39,019 * INFO * [92544] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/1/6
2015-08-06 20:47:42,137 * INFO * [92286] atomIncorp_taxaIncorp_abund/100/1/3 Finished with 0
2015-08-06 20:47:42,145 * INFO * [92568] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/20
2015-08-06 20:47:44,998 * INFO * [92197] atomIncorp_taxaIncorp_abund/100/1/17 Finished with 0
2015-08-06 20:47:45,006 * INFO * [92593] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/14
2015-08-06 20:47:57,216 * INFO * [92446] atomIncorp_taxaIncorp_abund/100/1/12 Finished with 0
2015-08-06 20:47:57,224 * INFO * [92682] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/7
2015-08-06 20:47:58,313 * INFO * [92332] atomIncorp_taxaIncorp_abund/100/1/13 Finished with 0
2015-08-06 20:47:58,320 * INFO * [92702] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/19
2015-08-06 20:48:04,255 * INFO * [92434] atomIncorp_taxaIncorp_abund/100/1/2 Finished with 0
2015-08-06 20:48:04,265 * INFO * [92738] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/18
2015-08-06 20:48:06,004 * INFO * [92500] atomIncorp_taxaIncorp_abund/100/1/4 Finished with 0
2015-08-06 20:48:06,014 * INFO * [92756] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/15
2015-08-06 20:48:09,434 * INFO * [92406] atomIncorp_taxaIncorp_abund/100/1/10 Finished with 0
2015-08-06 20:48:09,441 * INFO * [92792] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/11
2015-08-06 20:48:16,249 * INFO * [92544] atomIncorp_taxaIncorp_abund/100/1/6 Finished with 0
2015-08-06 20:48:16,260 * INFO * [92850] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/16
2015-08-06 20:48:25,309 * INFO * [92512] atomIncorp_taxaIncorp_abund/100/1/5 Finished with 0
2015-08-06 20:48:25,318 * INFO * [92920] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/9
2015-08-06 20:48:27,805 * INFO * [92702] atomIncorp_taxaIncorp_abund/100/5/19 Finished with 0
2015-08-06 20:48:27,815 * INFO * [92934] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/17
2015-08-06 20:48:27,835 * INFO * [92488] atomIncorp_taxaIncorp_abund/100/1/1 Finished with 0
2015-08-06 20:48:27,845 * INFO * [92939] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/8
2015-08-06 20:48:29,873 * INFO * [92593] atomIncorp_taxaIncorp_abund/100/5/14 Finished with 0
2015-08-06 20:48:29,880 * INFO * [92962] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/3
2015-08-06 20:48:30,150 * INFO * [92738] atomIncorp_taxaIncorp_abund/100/5/18 Finished with 0
2015-08-06 20:48:30,156 * INFO * [92974] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/13
2015-08-06 20:48:41,234 * INFO * [92792] atomIncorp_taxaIncorp_abund/100/5/11 Finished with 0
2015-08-06 20:48:41,244 * INFO * [93044] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/10
2015-08-06 20:48:50,594 * INFO * [92568] atomIncorp_taxaIncorp_abund/100/5/20 Finished with 0
2015-08-06 20:48:50,604 * INFO * [93120] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/2
2015-08-06 20:48:57,281 * INFO * [92850] atomIncorp_taxaIncorp_abund/100/5/16 Finished with 0
2015-08-06 20:48:57,291 * INFO * [93150] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/12
2015-08-06 20:48:57,397 * INFO * [92962] atomIncorp_taxaIncorp_abund/100/5/3 Finished with 0
2015-08-06 20:48:57,406 * INFO * [93162] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/1
2015-08-06 20:48:59,117 * INFO * [92974] atomIncorp_taxaIncorp_abund/100/5/13 Finished with 0
2015-08-06 20:48:59,127 * INFO * [93182] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/4
2015-08-06 20:49:00,761 * INFO * [92682] atomIncorp_taxaIncorp_abund/100/5/7 Finished with 0
2015-08-06 20:49:00,771 * INFO * [93194] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/5
2015-08-06 20:49:02,492 * INFO * [92920] atomIncorp_taxaIncorp_abund/100/5/9 Finished with 0
2015-08-06 20:49:02,502 * INFO * [93212] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/100/5/6
2015-08-06 20:49:02,956 * INFO * [92756] atomIncorp_taxaIncorp_abund/100/5/15 Finished with 0
2015-08-06 20:49:02,964 * INFO * [93224] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/20
2015-08-06 20:49:17,942 * INFO * [93120] atomIncorp_taxaIncorp_abund/100/5/2 Finished with 0
2015-08-06 20:49:17,952 * INFO * [93324] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/14
2015-08-06 20:49:25,811 * INFO * [93044] atomIncorp_taxaIncorp_abund/100/5/10 Finished with 0
2015-08-06 20:49:25,820 * INFO * [93376] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/7
2015-08-06 20:49:26,261 * INFO * [92939] atomIncorp_taxaIncorp_abund/100/5/8 Finished with 0
2015-08-06 20:49:26,272 * INFO * [93389] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/19
2015-08-06 20:49:31,293 * INFO * [92934] atomIncorp_taxaIncorp_abund/100/5/17 Finished with 0
2015-08-06 20:49:31,307 * INFO * [93428] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/18
2015-08-06 20:49:32,273 * INFO * [93182] atomIncorp_taxaIncorp_abund/100/5/4 Finished with 0
2015-08-06 20:49:32,283 * INFO * [93440] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/15
2015-08-06 20:49:33,886 * INFO * [93162] atomIncorp_taxaIncorp_abund/100/5/1 Finished with 0
2015-08-06 20:49:33,896 * INFO * [93452] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/11
2015-08-06 20:49:34,527 * INFO * [93194] atomIncorp_taxaIncorp_abund/100/5/5 Finished with 0
2015-08-06 20:49:34,536 * INFO * [93464] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/16
2015-08-06 20:49:36,630 * INFO * [93150] atomIncorp_taxaIncorp_abund/100/5/12 Finished with 0
2015-08-06 20:49:36,644 * INFO * [93498] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/9
2015-08-06 20:49:52,234 * INFO * [93224] atomIncorp_taxaIncorp_abund/25/50/20 Finished with 0
2015-08-06 20:49:52,243 * INFO * [93586] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/17
2015-08-06 20:49:55,818 * INFO * [93324] atomIncorp_taxaIncorp_abund/25/50/14 Finished with 0
2015-08-06 20:49:55,824 * INFO * [93652] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/8
2015-08-06 20:50:05,506 * INFO * [93464] atomIncorp_taxaIncorp_abund/25/50/16 Finished with 0
2015-08-06 20:50:05,519 * INFO * [93694] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/3
2015-08-06 20:50:06,688 * INFO * [93428] atomIncorp_taxaIncorp_abund/25/50/18 Finished with 0
2015-08-06 20:50:06,698 * INFO * [93714] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/13
2015-08-06 20:50:10,381 * INFO * [93212] atomIncorp_taxaIncorp_abund/100/5/6 Finished with 0
2015-08-06 20:50:10,394 * INFO * [93740] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/10
2015-08-06 20:50:11,725 * INFO * [93498] atomIncorp_taxaIncorp_abund/25/50/9 Finished with 0
2015-08-06 20:50:11,734 * INFO * [93776] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/2
2015-08-06 20:50:19,504 * INFO * [93440] atomIncorp_taxaIncorp_abund/25/50/15 Finished with 0
2015-08-06 20:50:19,515 * INFO * [93810] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/12
2015-08-06 20:50:20,084 * INFO * [93389] atomIncorp_taxaIncorp_abund/25/50/19 Finished with 0
2015-08-06 20:50:20,095 * INFO * [93822] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/1
2015-08-06 20:50:20,824 * INFO * [93586] atomIncorp_taxaIncorp_abund/25/50/17 Finished with 0
2015-08-06 20:50:20,837 * INFO * [93834] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/4
2015-08-06 20:50:27,007 * INFO * [93376] atomIncorp_taxaIncorp_abund/25/50/7 Finished with 0
2015-08-06 20:50:27,016 * INFO * [93862] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/5
2015-08-06 20:50:30,963 * INFO * [93652] atomIncorp_taxaIncorp_abund/25/50/8 Finished with 0
2015-08-06 20:50:30,972 * INFO * [93894] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/50/6
2015-08-06 20:50:31,681 * INFO * [93452] atomIncorp_taxaIncorp_abund/25/50/11 Finished with 0
2015-08-06 20:50:31,691 * INFO * [93906] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/20
2015-08-06 20:50:36,229 * INFO * [93694] atomIncorp_taxaIncorp_abund/25/50/3 Finished with 0
2015-08-06 20:50:36,239 * INFO * [93940] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/14
2015-08-06 20:50:53,723 * INFO * [93810] atomIncorp_taxaIncorp_abund/25/50/12 Finished with 0
2015-08-06 20:50:53,734 * INFO * [94077] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/7
2015-08-06 20:50:59,171 * INFO * [93822] atomIncorp_taxaIncorp_abund/25/50/1 Finished with 0
2015-08-06 20:50:59,183 * INFO * [94105] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/19
2015-08-06 20:50:59,425 * INFO * [93776] atomIncorp_taxaIncorp_abund/25/50/2 Finished with 0
2015-08-06 20:50:59,433 * INFO * [94117] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/18
2015-08-06 20:51:02,822 * INFO * [93714] atomIncorp_taxaIncorp_abund/25/50/13 Finished with 0
2015-08-06 20:51:02,832 * INFO * [94151] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/15
2015-08-06 20:51:03,940 * INFO * [93740] atomIncorp_taxaIncorp_abund/25/50/10 Finished with 0
2015-08-06 20:51:03,950 * INFO * [94163] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/11
2015-08-06 20:51:10,256 * INFO * [93894] atomIncorp_taxaIncorp_abund/25/50/6 Finished with 0
2015-08-06 20:51:10,267 * INFO * [94197] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/16
2015-08-06 20:51:12,583 * INFO * [93862] atomIncorp_taxaIncorp_abund/25/50/5 Finished with 0
2015-08-06 20:51:12,595 * INFO * [94223] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/9
2015-08-06 20:51:20,853 * INFO * [93834] atomIncorp_taxaIncorp_abund/25/50/4 Finished with 0
2015-08-06 20:51:20,862 * INFO * [94271] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/17
2015-08-06 20:51:22,494 * INFO * [93906] atomIncorp_taxaIncorp_abund/25/25/20 Finished with 0
2015-08-06 20:51:22,503 * INFO * [94289] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/8
2015-08-06 20:51:25,733 * INFO * [93940] atomIncorp_taxaIncorp_abund/25/25/14 Finished with 0
2015-08-06 20:51:25,744 * INFO * [94331] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/3
2015-08-06 20:51:33,009 * INFO * [94151] atomIncorp_taxaIncorp_abund/25/25/15 Finished with 0
2015-08-06 20:51:33,019 * INFO * [94367] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/13
2015-08-06 20:51:38,379 * INFO * [94077] atomIncorp_taxaIncorp_abund/25/25/7 Finished with 0
2015-08-06 20:51:38,391 * INFO * [94399] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/10
2015-08-06 20:51:43,943 * INFO * [94197] atomIncorp_taxaIncorp_abund/25/25/16 Finished with 0
2015-08-06 20:51:43,953 * INFO * [94441] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/2
2015-08-06 20:51:48,712 * INFO * [94117] atomIncorp_taxaIncorp_abund/25/25/18 Finished with 0
2015-08-06 20:51:48,720 * INFO * [94484] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/12
2015-08-06 20:51:54,146 * INFO * [94163] atomIncorp_taxaIncorp_abund/25/25/11 Finished with 0
2015-08-06 20:51:54,157 * INFO * [94528] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/1
2015-08-06 20:51:57,507 * INFO * [94223] atomIncorp_taxaIncorp_abund/25/25/9 Finished with 0
2015-08-06 20:51:57,527 * INFO * [94562] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/4
2015-08-06 20:51:58,238 * INFO * [94105] atomIncorp_taxaIncorp_abund/25/25/19 Finished with 0
2015-08-06 20:51:58,248 * INFO * [94574] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/5
2015-08-06 20:52:01,899 * INFO * [94331] atomIncorp_taxaIncorp_abund/25/25/3 Finished with 0
2015-08-06 20:52:01,907 * INFO * [94594] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/25/6
2015-08-06 20:52:09,462 * INFO * [94399] atomIncorp_taxaIncorp_abund/25/25/10 Finished with 0
2015-08-06 20:52:09,472 * INFO * [94628] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/20
2015-08-06 20:52:11,176 * INFO * [94289] atomIncorp_taxaIncorp_abund/25/25/8 Finished with 0
2015-08-06 20:52:11,192 * INFO * [94640] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/14
2015-08-06 20:52:12,399 * INFO * [94271] atomIncorp_taxaIncorp_abund/25/25/17 Finished with 0
2015-08-06 20:52:12,411 * INFO * [94652] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/7
2015-08-06 20:52:19,633 * INFO * [94367] atomIncorp_taxaIncorp_abund/25/25/13 Finished with 0
2015-08-06 20:52:19,644 * INFO * [94698] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/19
2015-08-06 20:52:28,866 * INFO * [94562] atomIncorp_taxaIncorp_abund/25/25/4 Finished with 0
2015-08-06 20:52:28,871 * INFO * [94774] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/18
2015-08-06 20:52:32,724 * INFO * [94594] atomIncorp_taxaIncorp_abund/25/25/6 Finished with 0
2015-08-06 20:52:32,734 * INFO * [94800] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/15
2015-08-06 20:52:49,445 * INFO * [94484] atomIncorp_taxaIncorp_abund/25/25/12 Finished with 0
2015-08-06 20:52:49,455 * INFO * [94926] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/11
2015-08-06 20:52:49,663 * INFO * [94698] atomIncorp_taxaIncorp_abund/25/10/19 Finished with 0
2015-08-06 20:52:49,674 * INFO * [94938] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/16
2015-08-06 20:52:53,248 * INFO * [94574] atomIncorp_taxaIncorp_abund/25/25/5 Finished with 0
2015-08-06 20:52:53,258 * INFO * [94950] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/9
2015-08-06 20:53:01,667 * INFO * [94774] atomIncorp_taxaIncorp_abund/25/10/18 Finished with 0
2015-08-06 20:53:01,673 * INFO * [95000] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/17
2015-08-06 20:53:02,741 * INFO * [94528] atomIncorp_taxaIncorp_abund/25/25/1 Finished with 0
2015-08-06 20:53:02,750 * INFO * [95012] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/8
2015-08-06 20:53:02,949 * INFO * [94441] atomIncorp_taxaIncorp_abund/25/25/2 Finished with 0
2015-08-06 20:53:02,957 * INFO * [95024] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/3
2015-08-06 20:53:05,264 * INFO * [94628] atomIncorp_taxaIncorp_abund/25/10/20 Finished with 0
2015-08-06 20:53:05,273 * INFO * [95056] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/13
2015-08-06 20:53:09,066 * INFO * [94652] atomIncorp_taxaIncorp_abund/25/10/7 Finished with 0
2015-08-06 20:53:09,076 * INFO * [95068] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/10
2015-08-06 20:53:11,669 * INFO * [94640] atomIncorp_taxaIncorp_abund/25/10/14 Finished with 0
2015-08-06 20:53:11,680 * INFO * [95094] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/2
2015-08-06 20:53:18,718 * INFO * [94800] atomIncorp_taxaIncorp_abund/25/10/15 Finished with 0
2015-08-06 20:53:18,729 * INFO * [95134] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/12
2015-08-06 20:53:27,942 * INFO * [94938] atomIncorp_taxaIncorp_abund/25/10/16 Finished with 0
2015-08-06 20:53:27,954 * INFO * [95200] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/1
2015-08-06 20:53:31,510 * INFO * [95000] atomIncorp_taxaIncorp_abund/25/10/17 Finished with 0
2015-08-06 20:53:31,521 * INFO * [95218] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/4
2015-08-06 20:53:37,680 * INFO * [94950] atomIncorp_taxaIncorp_abund/25/10/9 Finished with 0
2015-08-06 20:53:37,691 * INFO * [95258] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/5
2015-08-06 20:53:40,328 * INFO * [94926] atomIncorp_taxaIncorp_abund/25/10/11 Finished with 0
2015-08-06 20:53:40,336 * INFO * [95286] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/10/6
2015-08-06 20:53:42,114 * INFO * [95094] atomIncorp_taxaIncorp_abund/25/10/2 Finished with 0
2015-08-06 20:53:42,125 * INFO * [95306] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/20
2015-08-06 20:53:48,268 * INFO * [95056] atomIncorp_taxaIncorp_abund/25/10/13 Finished with 0
2015-08-06 20:53:48,276 * INFO * [95346] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/14
2015-08-06 20:53:59,040 * INFO * [95134] atomIncorp_taxaIncorp_abund/25/10/12 Finished with 0
2015-08-06 20:53:59,046 * INFO * [95432] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/7
2015-08-06 20:54:01,836 * INFO * [95012] atomIncorp_taxaIncorp_abund/25/10/8 Finished with 0
2015-08-06 20:54:01,845 * INFO * [95446] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/19
2015-08-06 20:54:03,554 * INFO * [95286] atomIncorp_taxaIncorp_abund/25/10/6 Finished with 0
2015-08-06 20:54:03,561 * INFO * [95471] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/18
2015-08-06 20:54:05,129 * INFO * [95024] atomIncorp_taxaIncorp_abund/25/10/3 Finished with 0
2015-08-06 20:54:05,137 * INFO * [95499] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/15
2015-08-06 20:54:12,945 * INFO * [95218] atomIncorp_taxaIncorp_abund/25/10/4 Finished with 0
2015-08-06 20:54:12,955 * INFO * [95562] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/11
2015-08-06 20:54:13,525 * INFO * [95306] atomIncorp_taxaIncorp_abund/25/1/20 Finished with 0
2015-08-06 20:54:13,532 * INFO * [95588] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/16
2015-08-06 20:54:23,867 * INFO * [95068] atomIncorp_taxaIncorp_abund/25/10/10 Finished with 0
2015-08-06 20:54:23,876 * INFO * [95727] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/9
2015-08-06 20:54:29,548 * INFO * [95200] atomIncorp_taxaIncorp_abund/25/10/1 Finished with 0
2015-08-06 20:54:29,557 * INFO * [95777] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/17
2015-08-06 20:54:30,155 * INFO * [95499] atomIncorp_taxaIncorp_abund/25/1/15 Finished with 0
2015-08-06 20:54:30,160 * INFO * [95789] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/8
2015-08-06 20:54:30,856 * INFO * [95471] atomIncorp_taxaIncorp_abund/25/1/18 Finished with 0
2015-08-06 20:54:30,863 * INFO * [95801] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/3
2015-08-06 20:54:40,091 * INFO * [95562] atomIncorp_taxaIncorp_abund/25/1/11 Finished with 0
2015-08-06 20:54:40,101 * INFO * [95871] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/13
2015-08-06 20:54:42,889 * INFO * [95258] atomIncorp_taxaIncorp_abund/25/10/5 Finished with 0
2015-08-06 20:54:42,897 * INFO * [95899] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/10
2015-08-06 20:54:48,852 * INFO * [95432] atomIncorp_taxaIncorp_abund/25/1/7 Finished with 0
2015-08-06 20:54:48,859 * INFO * [95941] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/2
2015-08-06 20:54:50,795 * INFO * [95446] atomIncorp_taxaIncorp_abund/25/1/19 Finished with 0
2015-08-06 20:54:50,801 * INFO * [95959] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/12
2015-08-06 20:54:51,807 * INFO * [95346] atomIncorp_taxaIncorp_abund/25/1/14 Finished with 0
2015-08-06 20:54:51,816 * INFO * [95979] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/1
2015-08-06 20:55:01,370 * INFO * [95727] atomIncorp_taxaIncorp_abund/25/1/9 Finished with 0
2015-08-06 20:55:01,379 * INFO * [96043] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/4
2015-08-06 20:55:02,520 * INFO * [95588] atomIncorp_taxaIncorp_abund/25/1/16 Finished with 0
2015-08-06 20:55:02,527 * INFO * [96072] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/5
2015-08-06 20:55:08,581 * INFO * [95871] atomIncorp_taxaIncorp_abund/25/1/13 Finished with 0
2015-08-06 20:55:08,592 * INFO * [96122] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/1/6
2015-08-06 20:55:15,249 * INFO * [95941] atomIncorp_taxaIncorp_abund/25/1/2 Finished with 0
2015-08-06 20:55:15,254 * INFO * [96172] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/20
2015-08-06 20:55:15,369 * INFO * [95777] atomIncorp_taxaIncorp_abund/25/1/17 Finished with 0
2015-08-06 20:55:15,375 * INFO * [96184] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/14
2015-08-06 20:55:17,385 * INFO * [95959] atomIncorp_taxaIncorp_abund/25/1/12 Finished with 0
2015-08-06 20:55:17,391 * INFO * [96202] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/7
2015-08-06 20:55:17,593 * INFO * [95801] atomIncorp_taxaIncorp_abund/25/1/3 Finished with 0
2015-08-06 20:55:17,600 * INFO * [96214] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/19
2015-08-06 20:55:23,023 * INFO * [95979] atomIncorp_taxaIncorp_abund/25/1/1 Finished with 0
2015-08-06 20:55:23,030 * INFO * [96234] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/18
2015-08-06 20:55:25,867 * INFO * [95789] atomIncorp_taxaIncorp_abund/25/1/8 Finished with 0
2015-08-06 20:55:25,872 * INFO * [96252] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/15
2015-08-06 20:55:32,419 * INFO * [96043] atomIncorp_taxaIncorp_abund/25/1/4 Finished with 0
2015-08-06 20:55:32,424 * INFO * [96322] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/11
2015-08-06 20:55:44,480 * INFO * [96172] atomIncorp_taxaIncorp_abund/25/5/20 Finished with 0
2015-08-06 20:55:44,487 * INFO * [96418] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/16
2015-08-06 20:55:45,616 * INFO * [96214] atomIncorp_taxaIncorp_abund/25/5/19 Finished with 0
2015-08-06 20:55:45,624 * INFO * [96430] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/9
2015-08-06 20:55:47,849 * INFO * [96234] atomIncorp_taxaIncorp_abund/25/5/18 Finished with 0
2015-08-06 20:55:47,856 * INFO * [96448] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/17
2015-08-06 20:55:47,951 * INFO * [96072] atomIncorp_taxaIncorp_abund/25/1/5 Finished with 0
2015-08-06 20:55:47,956 * INFO * [96460] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/8
2015-08-06 20:55:48,648 * INFO * [95899] atomIncorp_taxaIncorp_abund/25/1/10 Finished with 0
2015-08-06 20:55:48,655 * INFO * [96480] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/3
2015-08-06 20:55:53,282 * INFO * [96122] atomIncorp_taxaIncorp_abund/25/1/6 Finished with 0
2015-08-06 20:55:53,286 * INFO * [96498] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/13
2015-08-06 20:55:55,337 * INFO * [96202] atomIncorp_taxaIncorp_abund/25/5/7 Finished with 0
2015-08-06 20:55:55,343 * INFO * [96536] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/10
2015-08-06 20:55:56,145 * INFO * [96184] atomIncorp_taxaIncorp_abund/25/5/14 Finished with 0
2015-08-06 20:55:56,152 * INFO * [96554] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/2
2015-08-06 20:56:09,466 * INFO * [96460] atomIncorp_taxaIncorp_abund/25/5/8 Finished with 0
2015-08-06 20:56:09,473 * INFO * [96676] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/12
2015-08-06 20:56:10,567 * INFO * [96480] atomIncorp_taxaIncorp_abund/25/5/3 Finished with 0
2015-08-06 20:56:10,573 * INFO * [96702] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/1
2015-08-06 20:56:15,663 * INFO * [96252] atomIncorp_taxaIncorp_abund/25/5/15 Finished with 0
2015-08-06 20:56:15,669 * INFO * [96744] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/4
2015-08-06 20:56:18,226 * INFO * [96430] atomIncorp_taxaIncorp_abund/25/5/9 Finished with 0
2015-08-06 20:56:18,232 * INFO * [96764] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/5
2015-08-06 20:56:20,854 * INFO * [96448] atomIncorp_taxaIncorp_abund/25/5/17 Finished with 0
2015-08-06 20:56:20,859 * INFO * [96784] Started ./SIPSimRun.sh in atomIncorp_taxaIncorp_abund/25/5/6
2015-08-06 20:56:24,997 * INFO * [96322] atomIncorp_taxaIncorp_abund/25/5/11 Finished with 0
2015-08-06 20:56:25,373 * INFO * [96418] atomIncorp_taxaIncorp_abund/25/5/16 Finished with 0
2015-08-06 20:56:26,595 * INFO * [96498] atomIncorp_taxaIncorp_abund/25/5/13 Finished with 0
2015-08-06 20:56:29,912 * INFO * [96536] atomIncorp_taxaIncorp_abund/25/5/10 Finished with 0
2015-08-06 20:56:35,265 * INFO * [96554] atomIncorp_taxaIncorp_abund/25/5/2 Finished with 0



In [81]:

    
# aggregating confusion matrix data
## byClass
### dominant
!cd $workDir; \
    nestagg delim \
        -d atomIncorp_taxaIncorp_abund \
        -k percIncorp,percTaxa,rep \
        -o ./atomIncorp_taxaIncorp_abund/DESeq2-cMtx_dom_byClass.csv \
        DESeq2-cMtx_dom_byClass.csv

### rare
!cd $workDir; \
    nestagg delim \
        -d atomIncorp_taxaIncorp_abund \
        -k percIncorp,percTaxa,rep \
        -o ./atomIncorp_taxaIncorp_abund/DESeq2-cMtx_rare_byClass.csv \
        DESeq2-cMtx_rare_byClass.csv

Plotting accuracy

Dominant taxa



In [82]:

    
%%R -i workDir
setwd(workDir)

byClass = read.csv('./atomIncorp_taxaIncorp_abund/DESeq2-cMtx_dom_byClass.csv')
byClass %>% head









    





               X   byClass percIncorp percTaxa rep
1    Sensitivity 0.5000000         50       50  20
2    Specificity 1.0000000         50       50  20
3 Pos Pred Value 1.0000000         50       50  20
4 Neg Pred Value 0.4285714         50       50  20
5     Prevalence 0.7272727         50       50  20
6 Detection Rate 0.3636364         50       50  20



In [83]:

    
%%R -w 700 

col2keep = c('Balanced Accuracy', 'Sensitivity','Specificity')

byClass.f = byClass %>%
    filter(X %in% col2keep) %>%
    mutate(percIncorp = as.character(percIncorp),
           percTaxa = as.character(percTaxa))

byClass.f$percIncorp = factor(byClass.f$percIncorp, levels=sort(unique(as.numeric(byClass.f$percIncorp))))
byClass.f$percTaxa = factor(byClass.f$percTaxa, levels=sort(unique(as.numeric(byClass.f$percTaxa))))


ggplot(byClass.f, aes(percIncorp, byClass, fill=percTaxa)) +
    geom_boxplot(position='dodge') +
    labs(y='Value', x='Atom percent 13C') +
    facet_grid(X ~ .) +
    theme(
        text = element_text(size=16)
        )

Rare taxa



In [84]:

    
%%R -i workDir
setwd(workDir)

byClass = read.csv('./atomIncorp_taxaIncorp_abund/DESeq2-cMtx_rare_byClass.csv')
byClass %>% head









    





               X    byClass percIncorp percTaxa rep
1    Sensitivity 0.13725490         50       50  20
2    Specificity 1.00000000         50       50  20
3 Pos Pred Value 1.00000000         50       50  20
4 Neg Pred Value 0.52857143         50       50  20
5     Prevalence 0.50830565         50       50  20
6 Detection Rate 0.06976744         50       50  20



In [85]:

    
%%R -w 700 

col2keep = c('Balanced Accuracy', 'Sensitivity','Specificity')

byClass.f = byClass %>%
    filter(X %in% col2keep) %>%
    mutate(percIncorp = as.character(percIncorp),
           percTaxa = as.character(percTaxa))

byClass.f$percIncorp = factor(byClass.f$percIncorp, levels=sort(unique(as.numeric(byClass.f$percIncorp))))
byClass.f$percTaxa = factor(byClass.f$percTaxa, levels=sort(unique(as.numeric(byClass.f$percTaxa))))


ggplot(byClass.f, aes(percIncorp, byClass, fill=percTaxa)) +
    geom_boxplot(position='dodge') +
    labs(y='Value', x='Atom percent 13C') +
    facet_grid(X ~ .) +
    theme(
        text = element_text(size=16)
        )

Notes:

Dominants can produce higher sensitivity, but (likely) smaller sample size, so crap shoot on whether dominant taxon is in the optimal GC window for the DESeq2 analysis.
Rares essentially match whole-community accuracy.
- Likely due to sample size of rares (most of community for log-normal abundance distribution)

Questions:

What is the sample size of dominants and rares?

Sample size of dominants and rares

Method:
- Get number of taxa from dominant/rare-parsed DESeq2 object files



In [59]:

    
%%R -i workDir
setwd(workDir)

dom.files = grep('DESeq2_dom$', list.files('./atomIncorp_taxaIncorp_abund/', recursive=TRUE), value=TRUE)
rare.files = grep('DESeq2_rare$', list.files('./atomIncorp_taxaIncorp_abund/', recursive=TRUE), value=TRUE)

read_taxa = function(file.name, dir='atomIncorp_taxaIncorp_abund'){
    f = paste(c(dir, file.name), collapse='/')
    deseq.res = readRDS(f)
    n.taxa = length(unique(rownames(deseq.res)))
    return(n.taxa)
    }

dom.taxa = list()
for(f in dom.files){
    dom.taxa[[f]] = read_taxa(f)
    }

rare.taxa = list()
for(f in rare.files){
    rare.taxa[[f]] = read_taxa(f)
    }



In [60]:

    
%%R 
tbl.dom = as.data.frame(do.call(rbind, dom.taxa))
tbl.dom$abund = 'Dominant'
tbl.rare = as.data.frame(do.call(rbind, rare.taxa))
tbl.rare$abund = 'Rare'

tbl.dom.rare = rbind(tbl.dom, tbl.rare)
colnames(tbl.dom.rare)[1] = 'N.taxa'
tbl.dom.rare$file = rownames(tbl.dom.rare) 
tbl.dom.rare = tbl.dom.rare %>% 
    separate(file, c('percIncorp','percTaxa','rep','file'), sep='/') 
tbl.dom.rare %>% head









    





                                          N.taxa    abund percIncorp percTaxa
0/10/10/OTU_n2_abs1e9_sub-norm_DESeq2_dom     13 Dominant          0       10
0/10/11/OTU_n2_abs1e9_sub-norm_DESeq2_dom     12 Dominant          0       10
0/10/12/OTU_n2_abs1e9_sub-norm_DESeq2_dom     15 Dominant          0       10
0/10/13/OTU_n2_abs1e9_sub-norm_DESeq2_dom     12 Dominant          0       10
0/10/14/OTU_n2_abs1e9_sub-norm_DESeq2_dom     16 Dominant          0       10
0/10/15/OTU_n2_abs1e9_sub-norm_DESeq2_dom     11 Dominant          0       10
                                          rep                              file
0/10/10/OTU_n2_abs1e9_sub-norm_DESeq2_dom  10 OTU_n2_abs1e9_sub-norm_DESeq2_dom
0/10/11/OTU_n2_abs1e9_sub-norm_DESeq2_dom  11 OTU_n2_abs1e9_sub-norm_DESeq2_dom
0/10/12/OTU_n2_abs1e9_sub-norm_DESeq2_dom  12 OTU_n2_abs1e9_sub-norm_DESeq2_dom
0/10/13/OTU_n2_abs1e9_sub-norm_DESeq2_dom  13 OTU_n2_abs1e9_sub-norm_DESeq2_dom
0/10/14/OTU_n2_abs1e9_sub-norm_DESeq2_dom  14 OTU_n2_abs1e9_sub-norm_DESeq2_dom
0/10/15/OTU_n2_abs1e9_sub-norm_DESeq2_dom  15 OTU_n2_abs1e9_sub-norm_DESeq2_dom



In [61]:

    
%%R -w 700 -h 400

tbl.dom.rare$percIncorp = factor(tbl.dom.rare$percIncorp, levels=sort(unique(as.numeric(tbl.dom.rare$percIncorp))))
tbl.dom.rare$percTaxa = factor(tbl.dom.rare$percTaxa, levels=sort(unique(as.numeric(tbl.dom.rare$percTaxa))))

ggplot(tbl.dom.rare, aes(percIncorp, N.taxa, fill=percTaxa)) +
    geom_boxplot(position='dodge') +
    labs(y='Number of taxa', x='Atom percent 13C') +
    facet_grid(abund ~ ., scales='free_y') +
    theme(
        text = element_text(size=16)
        )

Notes:

Figure is showing number of taxa in each group
Dominant n-taxa very low (mean values) with a high variance

Plotting sensitivity ~ taxon_abundance

Method:
- table join: DESeq res file & BD-shift
  - join on taxon
- use cutoffs to select which taxa 'incorporated'
  - padj < 0.1
- compare DESeq result to true result
  - TP,FP,TN,FN
Figure:
- axes: taxon ~ abundance (pointrange: replicates)
  - ordered by abundance
- color by classification (TP,FP,TN,FN)
- facet: percIncorp ~ percTaxa



In [ ]:

    
%%bash -s "$R_dir"

find atomIncorp_taxaIncorp_abund/ -name "*DESeq2" | \
    perl -pe 's/(.+\/).+/\1/' | \
    xargs -P 8 -I % bash -c \
    "$1DESeq2_addInfo.r %OTU_n2_abs1e9_sub-norm_DESeq2 %comm.txt %ampFrags_kde_dif_incorp_BD-shift.txt > %OTU_n2_abs1e9_sub-norm_DESeq2_info"



In [25]:

    
%%R -i workDir
setwd(workDir)

deseq.files = grep('_DESeq2_info$', list.files('./atomIncorp_taxaIncorp_abund/', recursive=TRUE), value=TRUE)


tbl.l = list()
for(f in deseq.files){
    f = paste(c('./atomIncorp_taxaIncorp_abund/', f), collapse='/')
    tbl.l[[f]] = readRDS(f) %>% mutate(file = f)
    }

tbl = do.call(rbind, tbl.l)
rownames(tbl) = seq(1,nrow(tbl))

tbl %>% head









    





    baseMean log2FoldChange     lfcSE       stat    pvalue      padj         p
1  0.5049108     0.11107666 0.2718697 0.00000000 0.6953218 0.9936258 0.6953218
2 14.5871544    -0.26250401 0.3395417 0.00000000 0.9344016 0.9936258 0.9344016
3  0.0000000             NA        NA         NA        NA        NA        NA
4  3.7093265     0.27897603 0.4076513 0.07108044 0.4716669 0.9936258 0.4716669
5  2.2722084    -0.16705365 0.3580337 0.00000000 0.8779590 0.9936258 0.8779590
6  9.7317017     0.03058377 0.3786109 0.00000000 0.7188841 0.9936258 0.7188841
    padj.BH                                 taxon lib1 lib2 BD_shift
1 0.9936258        Acaryochloris_marina_MBIC11017   NA    2        0
2 0.9936258  Acetobacter_pasteurianus_IFO_3283-12   NA    2        0
3        NA     Acetohalobium_arabaticum_DSM_5501   NA    2        0
4 0.9936258         Achromobacter_xylosoxidans_A8   NA    2        0
5 0.9936258  Acidaminococcus_fermentans_DSM_20731   NA    2        0
6 0.9936258 Acidimicrobium_ferrooxidans_DSM_10331   NA    2        0
  mean_rel_abund_perc rank
1         0.130105629 1076
2         0.077478995 1004
3         0.009772099  575
4         0.020127186  754
5         0.016309341  699
6         0.049043241  932
                                                                       file
1 ./atomIncorp_taxaIncorp_abund//0/10/10/OTU_n2_abs1e9_sub-norm_DESeq2_info
2 ./atomIncorp_taxaIncorp_abund//0/10/10/OTU_n2_abs1e9_sub-norm_DESeq2_info
3 ./atomIncorp_taxaIncorp_abund//0/10/10/OTU_n2_abs1e9_sub-norm_DESeq2_info
4 ./atomIncorp_taxaIncorp_abund//0/10/10/OTU_n2_abs1e9_sub-norm_DESeq2_info
5 ./atomIncorp_taxaIncorp_abund//0/10/10/OTU_n2_abs1e9_sub-norm_DESeq2_info
6 ./atomIncorp_taxaIncorp_abund//0/10/10/OTU_n2_abs1e9_sub-norm_DESeq2_info



In [33]:

    
%%R
tbl.e = tbl %>%
    mutate(file = gsub('.+//','', file)) %>%
    separate(file, c('percIncorp','percTaxa','rep','file'), sep='/') %>%
    unite(percIncorp_percTaxa, percIncorp, percTaxa, sep='_', remove=FALSE)
tbl.e %>% head









    





    baseMean log2FoldChange     lfcSE       stat    pvalue      padj         p
1  0.5049108     0.11107666 0.2718697 0.00000000 0.6953218 0.9936258 0.6953218
2 14.5871544    -0.26250401 0.3395417 0.00000000 0.9344016 0.9936258 0.9344016
3  0.0000000             NA        NA         NA        NA        NA        NA
4  3.7093265     0.27897603 0.4076513 0.07108044 0.4716669 0.9936258 0.4716669
5  2.2722084    -0.16705365 0.3580337 0.00000000 0.8779590 0.9936258 0.8779590
6  9.7317017     0.03058377 0.3786109 0.00000000 0.7188841 0.9936258 0.7188841
    padj.BH                                 taxon lib1 lib2 BD_shift
1 0.9936258        Acaryochloris_marina_MBIC11017   NA    2        0
2 0.9936258  Acetobacter_pasteurianus_IFO_3283-12   NA    2        0
3        NA     Acetohalobium_arabaticum_DSM_5501   NA    2        0
4 0.9936258         Achromobacter_xylosoxidans_A8   NA    2        0
5 0.9936258  Acidaminococcus_fermentans_DSM_20731   NA    2        0
6 0.9936258 Acidimicrobium_ferrooxidans_DSM_10331   NA    2        0
  mean_rel_abund_perc rank percIncorp_percTaxa percIncorp percTaxa rep
1         0.130105629 1076                0_10          0       10  10
2         0.077478995 1004                0_10          0       10  10
3         0.009772099  575                0_10          0       10  10
4         0.020127186  754                0_10          0       10  10
5         0.016309341  699                0_10          0       10  10
6         0.049043241  932                0_10          0       10  10
                                file
1 OTU_n2_abs1e9_sub-norm_DESeq2_info
2 OTU_n2_abs1e9_sub-norm_DESeq2_info
3 OTU_n2_abs1e9_sub-norm_DESeq2_info
4 OTU_n2_abs1e9_sub-norm_DESeq2_info
5 OTU_n2_abs1e9_sub-norm_DESeq2_info
6 OTU_n2_abs1e9_sub-norm_DESeq2_info



In [34]:

    
%%R
BD.shift.cut = 0.05
padj.cut = 0.1


clsfy = function(guess,known){
    if(is.na(guess) | is.na(known)){
        return(NA)
        }
    if(guess == TRUE){
        if(guess == known){
            return('TP')
            } else {
            return('FP')
            }
        } else
    if(guess == FALSE){
        if(guess == known){
            return('TN')
            } else {
            return('FN')
            }
        } else {
        stop('Error: true or false needed')
        }
    }

tbl.e = tbl.e %>% 
    mutate(true_incorp = BD_shift > BD.shift.cut,
           DESeq_incorp = padj < padj.cut,
           cls = mapply(clsfy, DESeq_incorp, true_incorp)) 
    
tbl.e %>% head









    





    baseMean log2FoldChange     lfcSE       stat    pvalue      padj         p
1  0.5049108     0.11107666 0.2718697 0.00000000 0.6953218 0.9936258 0.6953218
2 14.5871544    -0.26250401 0.3395417 0.00000000 0.9344016 0.9936258 0.9344016
3  0.0000000             NA        NA         NA        NA        NA        NA
4  3.7093265     0.27897603 0.4076513 0.07108044 0.4716669 0.9936258 0.4716669
5  2.2722084    -0.16705365 0.3580337 0.00000000 0.8779590 0.9936258 0.8779590
6  9.7317017     0.03058377 0.3786109 0.00000000 0.7188841 0.9936258 0.7188841
    padj.BH                                 taxon lib1 lib2 BD_shift
1 0.9936258        Acaryochloris_marina_MBIC11017   NA    2        0
2 0.9936258  Acetobacter_pasteurianus_IFO_3283-12   NA    2        0
3        NA     Acetohalobium_arabaticum_DSM_5501   NA    2        0
4 0.9936258         Achromobacter_xylosoxidans_A8   NA    2        0
5 0.9936258  Acidaminococcus_fermentans_DSM_20731   NA    2        0
6 0.9936258 Acidimicrobium_ferrooxidans_DSM_10331   NA    2        0
  mean_rel_abund_perc rank percIncorp_percTaxa percIncorp percTaxa rep
1         0.130105629 1076                0_10          0       10  10
2         0.077478995 1004                0_10          0       10  10
3         0.009772099  575                0_10          0       10  10
4         0.020127186  754                0_10          0       10  10
5         0.016309341  699                0_10          0       10  10
6         0.049043241  932                0_10          0       10  10
                                file true_incorp DESeq_incorp  cls
1 OTU_n2_abs1e9_sub-norm_DESeq2_info       FALSE        FALSE   TN
2 OTU_n2_abs1e9_sub-norm_DESeq2_info       FALSE        FALSE   TN
3 OTU_n2_abs1e9_sub-norm_DESeq2_info       FALSE           NA <NA>
4 OTU_n2_abs1e9_sub-norm_DESeq2_info       FALSE        FALSE   TN
5 OTU_n2_abs1e9_sub-norm_DESeq2_info       FALSE        FALSE   TN
6 OTU_n2_abs1e9_sub-norm_DESeq2_info       FALSE        FALSE   TN



In [35]:

    
%%R
tbl.e$taxon = reorder(tbl.e$taxon, dense_rank(tbl.e$mean_rel_abund_perc))
tbl.e$percIncorp = factor(tbl.e$percIncorp, levels=sort(unique(as.numeric(tbl.e$percIncorp))))
tbl.e$percTaxa = factor(tbl.e$percTaxa, levels=sort(unique(as.numeric(tbl.e$percTaxa))))



In [40]:

    
%%R -w 1000

ggplot(tbl.e, aes(taxon, mean_rel_abund_perc, color=cls)) +
    geom_point(alpha=0.5) +
    facet_grid(percIncorp ~ percTaxa) +
    theme(
        text = element_text(size=16),
        axis.text.x = element_blank()
        )



In [52]:

    
%%R

clsfy = function(guess,known){
    if(is.na(guess) | is.na(known)){
        return(NA)
        }
    if(guess == TRUE){
        if(guess == known){
            return(1)
            } else {
            return(NA)
            }
        } else
    if(guess == FALSE){
        if(guess == known){
            return(NA)
            } else {
            return(0)
            }
        } else {
        stop('Error: true or false needed')
        }
    }

tbl.s.c = tbl.e %>%
    mutate(TP_FN = mapply(clsfy, DESeq_incorp, true_incorp)) %>%
    filter(! is.na(TP_FN)) %>%
    group_by(percIncorp, percTaxa) %>%
    summarize(cor.pearson = cor(mean_rel_abund_perc, TP_FN))

tbl.s.c %>% head









    





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

  percIncorp percTaxa cor.pearson
1         25        1 -0.03261236
2         25        5 -0.10158500
3         25       10 -0.08790304
4         25       25 -0.02180432
5         25       50  0.02516361
6         50        1 -0.20735579



In [64]:

    
%%R -w 600 -h 350
ggplot(tbl.s.c, aes(percIncorp, cor.pearson, fill=percTaxa)) +
    geom_bar(stat='identity', position='dodge', width=0.5) +
    labs(x='Atom percent 13C', y='r_pb', title='Point-biserial correlation coefficients') +
    theme(
        text = element_text(size=16)
        )

Notes:

Suggests that the correlation between sensitivity and taxon abundance is dependant on % atom incorp & percent of taxa that incorporated
- If only a few incorporator taxa, sensitivity will be poor regardless of abundance.
- Higher % atom produces weak positive correlation between taxon abundance and correct classification.
Tecnically, values are point-biserial correlation coefficients (not pearson)

SANDBOX



In [170]:

    
%%R -i workDir
setwd(workDir)

x.deseq = './validation/OTU_n2_abs1e10_sub20000_DESeq2'
deseq.res = readRDS(x.deseq)
deseq.res = as.data.frame(deseq.res)
deseq.res$taxon = rownames(deseq.res)
deseq.res %>% head









    





                                    baseMean log2FoldChange    lfcSE      stat
Acetohalobium_arabaticum_DSM_5501  0.4745836      0.9200834 1.394946 0.4803651
Acidovorax_citrulli_AAC00-1        3.2902741     -4.6553395 1.275818 0.0000000
Acidovorax_ebreus_TPSY             4.8031896     -1.0010777 1.176846 0.0000000
Aeromonas_hydrophila_AL09-71       0.7088409      0.5138864 1.270017 0.2077818
Alkalilimnicola_ehrlichii_MLHE-1  28.0436962     -1.2126332 1.274566 0.0000000
Alkaliphilus_oremlandii_OhILAs    29.5094790      0.5352219 1.697529 0.1680218
                                     pvalue padj         p padj.BH
Acetohalobium_arabaticum_DSM_5501 0.3154839    1 0.3154839       1
Acidovorax_citrulli_AAC00-1       0.9999397    1 0.9999397       1
Acidovorax_ebreus_TPSY            0.8561264    1 0.8561264       1
Aeromonas_hydrophila_AL09-71      0.4176997    1 0.4176997       1
Alkalilimnicola_ehrlichii_MLHE-1  0.8744236    1 0.8744236       1
Alkaliphilus_oremlandii_OhILAs    0.4332831    1 0.4332831       1
                                                              taxon
Acetohalobium_arabaticum_DSM_5501 Acetohalobium_arabaticum_DSM_5501
Acidovorax_citrulli_AAC00-1             Acidovorax_citrulli_AAC00-1
Acidovorax_ebreus_TPSY                       Acidovorax_ebreus_TPSY
Aeromonas_hydrophila_AL09-71           Aeromonas_hydrophila_AL09-71
Alkalilimnicola_ehrlichii_MLHE-1   Alkalilimnicola_ehrlichii_MLHE-1
Alkaliphilus_oremlandii_OhILAs       Alkaliphilus_oremlandii_OhILAs



In [171]:

    
%%R -i workDir
setwd(workDir) 

x.comm = 'validation/comm.txt'
comm = read.delim(x.comm, sep='\t')
comm.s = comm %>%
    group_by(taxon_name) %>%
    summarize(mean_rel_abund_perc = mean(rel_abund_perc)) %>%
    mutate(rank = dense_rank(mean_rel_abund_perc))
comm.s %>% head









    





Source: local data frame [6 x 3]

                            taxon_name mean_rel_abund_perc rank
1       Acaryochloris_marina_MBIC11017         0.089773401 1010
2       Acetobacterium_woodii_DSM_1030         0.013390418  609
3 Acetobacter_pasteurianus_IFO_3283-12         0.003064792  270
4    Acetohalobium_arabaticum_DSM_5501         0.058114601  928
5         Acholeplasma_laidlawii_PG-8A         0.004121299  323
6        Achromobacter_xylosoxidans_A8         0.024560238  752



In [172]:

    
%%R -i workDir
setwd(workDir) 

x.BD = 'validation/ampFrags_kde_dif_incorp_BD-shift.txt'
BD.shift = read.delim(x.BD, sep='\t')
BD.shift = BD.shift %>% 
    filter(lib2 == 2)
BD.shift %>% head









    





  lib1 lib2                              taxon BD_shift
1   NA    2         Vibrio_vulnificus_MO6-24_O        0
2   NA    2        Caldisericum_exile_AZM16c01      NaN
3   NA    2        Spiroplasma_taiwanense_CT-1        0
4   NA    2 Thermoanaerobacter_wiegelii_Rt8_B1        0
5   NA    2       Anabaena_cylindrica_PCC_7122        0
6   NA    2    Haemophilus_parainfluenzae_T3T1        0



In [173]:

    
%%R

tbl.j = inner_join(deseq.res, BD.shift, c('taxon' = 'taxon'))
tbl.j = inner_join(tbl.j, comm.s, c('taxon' = 'taxon_name'))
tbl.j %>% head









    





    baseMean log2FoldChange    lfcSE      stat    pvalue padj         p padj.BH
1  0.4745836      0.9200834 1.394946 0.4803651 0.3154839    1 0.3154839       1
2  3.2902741     -4.6553395 1.275818 0.0000000 0.9999397    1 0.9999397       1
3  4.8031896     -1.0010777 1.176846 0.0000000 0.8561264    1 0.8561264       1
4  0.7088409      0.5138864 1.270017 0.2077818 0.4176997    1 0.4176997       1
5 28.0436962     -1.2126332 1.274566 0.0000000 0.8744236    1 0.8744236       1
6 29.5094790      0.5352219 1.697529 0.1680218 0.4332831    1 0.4332831       1
                              taxon lib1 lib2  BD_shift mean_rel_abund_perc
1 Acetohalobium_arabaticum_DSM_5501   NA    2 0.0000000          0.05811460
2       Acidovorax_citrulli_AAC00-1   NA    2 0.9994683          0.07152763
3            Acidovorax_ebreus_TPSY   NA    2 0.0000000          0.14267760
4      Aeromonas_hydrophila_AL09-71   NA    2 0.9968581          0.02364744
5  Alkalilimnicola_ehrlichii_MLHE-1   NA    2 0.0000000          0.77596664
6    Alkaliphilus_oremlandii_OhILAs   NA    2 0.0000000          1.29218348
  rank
1  928
2  970
3 1068
4  745
5 1187
6 1199



In [174]:

    
%%R
BD.shift.cut = 0.05
padj.cut = 0.1


clsfy = function(guess,known){
    if(guess == TRUE){
        if(guess == known){
            return('TP')
            } else {
            return('FP')
            }
        } else
    if(guess == FALSE){
        if(guess == known){
            return('TN')
            } else {
            return('FN')
            }
        } else {
        stop('Error: true or false needed')
        }
    }

tbl.j = tbl.j %>% 
    mutate(true_incorp = BD_shift > BD.shift.cut,
           DESeq_incorp = padj < padj.cut,
           cls = mapply(clsfy, DESeq_incorp, true_incorp)) 
    
tbl.j %>% head









    





    baseMean log2FoldChange    lfcSE      stat    pvalue padj         p padj.BH
1  0.4745836      0.9200834 1.394946 0.4803651 0.3154839    1 0.3154839       1
2  3.2902741     -4.6553395 1.275818 0.0000000 0.9999397    1 0.9999397       1
3  4.8031896     -1.0010777 1.176846 0.0000000 0.8561264    1 0.8561264       1
4  0.7088409      0.5138864 1.270017 0.2077818 0.4176997    1 0.4176997       1
5 28.0436962     -1.2126332 1.274566 0.0000000 0.8744236    1 0.8744236       1
6 29.5094790      0.5352219 1.697529 0.1680218 0.4332831    1 0.4332831       1
                              taxon lib1 lib2  BD_shift mean_rel_abund_perc
1 Acetohalobium_arabaticum_DSM_5501   NA    2 0.0000000          0.05811460
2       Acidovorax_citrulli_AAC00-1   NA    2 0.9994683          0.07152763
3            Acidovorax_ebreus_TPSY   NA    2 0.0000000          0.14267760
4      Aeromonas_hydrophila_AL09-71   NA    2 0.9968581          0.02364744
5  Alkalilimnicola_ehrlichii_MLHE-1   NA    2 0.0000000          0.77596664
6    Alkaliphilus_oremlandii_OhILAs   NA    2 0.0000000          1.29218348
  rank true_incorp DESeq_incorp cls
1  928       FALSE        FALSE  TN
2  970        TRUE        FALSE  FN
3 1068       FALSE        FALSE  TN
4  745        TRUE        FALSE  FN
5 1187       FALSE        FALSE  TN
6 1199       FALSE        FALSE  TN



In [175]:

    
%%R -w 900

tbl.j$taxon = reorder(tbl.j$taxon, tbl.j$mean_rel_abund_perc)

ggplot(tbl.j, aes(taxon, mean_rel_abund_perc, color=cls)) +
    geom_point()



In [ ]:

    
%%R -i workDir
setwd(workDir)

deseq.res = readRDS('./validation/OTU_n2_abs1e10_sub20000_DESeq2')



In [17]:

    
%%R

comm = read.delim('./validation/comm.txt', sep='\t')
comm.s = comm %>%
    group_by(taxon_name) %>%
    summarize(mean_rel_abund_perc = mean(rel_abund_perc))
comm.s %>% head









    





Source: local data frame [6 x 2]

                            taxon_name mean_rel_abund_perc
1       Acaryochloris_marina_MBIC11017         0.089773401
2       Acetobacterium_woodii_DSM_1030         0.013390418
3 Acetobacter_pasteurianus_IFO_3283-12         0.003064792
4    Acetohalobium_arabaticum_DSM_5501         0.058114601
5         Acholeplasma_laidlawii_PG-8A         0.004121299
6        Achromobacter_xylosoxidans_A8         0.024560238



In [21]:

    
%%R
tmp = deseq.res %>%
    as.data.frame() 
tmp$taxon_name = rownames(tmp)

tmp = inner_join(tmp, comm.s, c('taxon_name' = 'taxon_name'))
tmp = tmp %>%
    mutate(dom_rare = mean_rel_abund_perc > 1)

tmp %>% head









    





    baseMean log2FoldChange    lfcSE      stat    pvalue padj         p padj.BH
1  0.4745836      0.9200834 1.394946 0.4803651 0.3154839    1 0.3154839       1
2  3.2902741     -4.6553395 1.275818 0.0000000 0.9999397    1 0.9999397       1
3  4.8031896     -1.0010777 1.176846 0.0000000 0.8561264    1 0.8561264       1
4  0.7088409      0.5138864 1.270017 0.2077818 0.4176997    1 0.4176997       1
5 28.0436962     -1.2126332 1.274566 0.0000000 0.8744236    1 0.8744236       1
6 29.5094790      0.5352219 1.697529 0.1680218 0.4332831    1 0.4332831       1
                         taxon_name mean_rel_abund_perc dom_rare
1 Acetohalobium_arabaticum_DSM_5501          0.05811460    FALSE
2       Acidovorax_citrulli_AAC00-1          0.07152763    FALSE
3            Acidovorax_ebreus_TPSY          0.14267760    FALSE
4      Aeromonas_hydrophila_AL09-71          0.02364744    FALSE
5  Alkalilimnicola_ehrlichii_MLHE-1          0.77596664    FALSE
6    Alkaliphilus_oremlandii_OhILAs          1.29218348     TRUE



In [22]:

    
%%R
tmp %>% filter(dom_rare == FALSE) %>% nrow %>% print
tmp %>% filter(dom_rare == TRUE) %>% nrow %>% print



In [ ]: