Analysing simulated and empirical datasets with stacks, pyrad, and ipyrad

This ipython notebook will provide a completely reproducible record of all the analyses for the ipyrad manuscript.

All analyses were performed on a 40 core Intel(R) Xeon(R) CPU E5-2680 v2 @ 2.80GHz Silicon Mechanics compute node with 120GB of main memory running CentOS Linux release 7.1.1503.

  • Insert thanks to the CCNY scientific computing cluster folks here

Notebook Tunnels

Mostly notes for myself, since my cluster config is complicated. To get a connection to a notebook on a compute node I have to bounce of 2 different machines, a gateway to get on campus, then another gateway (head hpc node) so I can talk to the cluster. The ssh commands will spawn processes in the background to shuttle communication between the ports. Kinda fancy.

On the cluster compute node (where you actually want to do the work) run:

ipython notebook --no-browser --port=8888 &

On the cluster head node run this to forward connections from the campus to a node inside the hpc infrastructure:

ssh -N -f -L localhost:8888:localhost:8888 <[email protected]<compute_node>

On your gateway box run:

ssh -N -f -L localhost:8887:localhost:8888 <username>@<head_node>


Prerequisites (download and install data and executables)

In [1]:
import shutil
import glob
import sys
import os

## Set the default directories for exec and data. 
WORK_DIR="/home/iovercast/manuscript-analysis/"
EMPERICAL_DATA_DIR=os.path.join(WORK_DIR, "example_empirical_rad/")
SIMULATION_DATA_DIR=os.path.join(WORK_DIR, "simulated_data")
IPYRAD_DIR=os.path.join(WORK_DIR, "ipyrad/")
PYRAD_DIR=os.path.join(WORK_DIR, "pyrad/")
STACKS_DIR=os.path.join(WORK_DIR, "stacks/")
AFTRRAD_DIR=os.path.join(WORK_DIR, "aftrRAD/")
DDOCENT_DIR=os.path.join(WORK_DIR, "dDocent/")

## (emprical data dir will be created for us when we untar it)
for dir in [WORK_DIR, IPYRAD_DIR, PYRAD_DIR, STACKS_DIR, AFTRRAD_DIR, DDOCENT_DIR]:
    if not os.path.exists(dir):
        os.makedirs(dir)

## Empirical output directories
IPYRAD_OUTPUT=os.path.join(IPYRAD_DIR, "REALDATA/")
PYRAD_OUTPUT=os.path.join(PYRAD_DIR, "REALDATA/")
STACKS_OUTPUT=os.path.join(STACKS_DIR, "REALDATA/")
STACKS_GAP_OUT=os.path.join(STACKS_OUTPUT, "gapped/")
STACKS_UNGAP_OUT=os.path.join(STACKS_OUTPUT, "ungapped/")
STACKS_DEFAULT_OUT=os.path.join(STACKS_OUTPUT, "default/")
AFTRRAD_OUTPUT=os.path.join(AFTRRAD_DIR, "REALDATA")
DDOCENT_OUTPUT=os.path.join(DDOCENT_DIR, "REALDATA")

## Make the empirical output directories if they don't already exist
for dir in [IPYRAD_OUTPUT, PYRAD_OUTPUT, STACKS_OUTPUT,\
            STACKS_GAP_OUT, STACKS_UNGAP_OUT, STACKS_DEFAULT_OUT, AFTRRAD_OUTPUT, DDOCENT_OUTPUT]:
    if not os.path.exists(dir):
        os.makedirs(dir)

os.chdir(WORK_DIR)
In [4]:
### Fetch the pedicularis data

##curl grabs the data from a public dropbox url
## the curl command uses an upper-case o argument, not a zero.
!curl -LkO https://dl.dropboxusercontent.com/u/2538935/example_empirical_rad.tar.gz

## the tar command decompresses the data directory
!tar -xvzf example_empirical_rad.tar.gz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 1042M  100 1042M    0     0  17.8M      0  0:00:58  0:00:58 --:--:-- 14.5M
example_empirical_rad/
example_empirical_rad/38362_rex.fastq.gz
example_empirical_rad/32082_przewalskii.fastq.gz
example_empirical_rad/40578_rex.fastq.gz
example_empirical_rad/30686_cyathophylla.fastq.gz
example_empirical_rad/39618_rex.fastq.gz
example_empirical_rad/41954_cyathophylloides.fastq.gz
example_empirical_rad/41478_cyathophylloides.fastq.gz
example_empirical_rad/33588_przewalskii.fastq.gz
example_empirical_rad/35855_rex.fastq.gz
example_empirical_rad/35236_rex.fastq.gz
example_empirical_rad/29154_superba.fastq.gz
example_empirical_rad/30556_thamno.fastq.gz
example_empirical_rad/33413_thamno.fastq.gz
In [195]:
## The original Helocnius analysis from pyrad v3
## Fetch the heliconius genome and rad data
##
## Davey, John W., et al. "Major improvements to the Heliconius melpomene 
## genome assembly used to confirm 10 chromosome fusion events in 6 
## million years of butterfly evolution." G3: Genes| Genomes| Genetics 6.3
## (2016): 695-708.

!curl -LkO http://butterflygenome.org/sites/default/files/Hmel2-0_Release_20160201.tgz
!tar -xvzf Hmel2-0_Release_20160201.tgz

## Several RAD datasets are available
##
## Heliconius Genome Consortium. (2012). Butterfly genome reveals 
## promiscuous exchange of mimicry adaptations among species. 
## Nature, 487(7405), 94-98.
## European Nucleotide Archive, Accession ERP000991
## Heliconius melpomene melpomene x Heliconius melpomene rosina - ERP000993

## And from the Davey et al 2016
## European Nucleotide Archive (ENA), accession PRJEB11288
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 93.6M  100 93.6M    0     0  12.1M      0  0:00:07  0:00:07 --:--:-- 14.8M
./._Hmel2
Hmel2/
Hmel2/._annotation
Hmel2/annotation/
Hmel2/._ChangeLog.txt
Hmel2/ChangeLog.txt
Hmel2/._Hmel2.fa
Hmel2/Hmel2.fa
Hmel2/._Hmel_mtDNA.fa
Hmel2/Hmel_mtDNA.fa
Hmel2/._maps
Hmel2/maps/
Hmel2/._README.txt
Hmel2/README.txt
Hmel2/._repeats
Hmel2/repeats/
Hmel2/._transfer
Hmel2/transfer/
Hmel2/transfer/._Hmel1-1_Hmel2.chain
Hmel2/transfer/Hmel1-1_Hmel2.chain
Hmel2/transfer/._Hmel2_broken.gff
Hmel2/transfer/Hmel2_broken.gff
Hmel2/transfer/._Hmel2_removed.gff
Hmel2/transfer/Hmel2_removed.gff
Hmel2/transfer/._Hmel2_transfer_new.tsv
Hmel2/transfer/Hmel2_transfer_new.tsv
Hmel2/transfer/._Hmel2_transfer_old.tsv
Hmel2/transfer/Hmel2_transfer_old.tsv
Hmel2/repeats/._Hmel.all.named.final.1-31.lib
Hmel2/repeats/Hmel.all.named.final.1-31.lib
Hmel2/maps/._Hmel2.gaps.bed
Hmel2/maps/Hmel2.gaps.bed
Hmel2/maps/._Hmel2_chromosome_linkage.tsv
Hmel2/maps/Hmel2_chromosome_linkage.tsv
Hmel2/maps/._Hmel2_chromosomes.agp
Hmel2/maps/Hmel2_chromosomes.agp
Hmel2/maps/._Hmel2_scaffold_linkage.tsv
Hmel2/maps/Hmel2_scaffold_linkage.tsv
Hmel2/maps/._Hmel2_scaffolds.agp
Hmel2/maps/Hmel2_scaffolds.agp
Hmel2/annotation/._Hmel2.gff
Hmel2/annotation/Hmel2.gff
Hmel2/annotation/._Hmel2_cds.fa
Hmel2/annotation/Hmel2_cds.fa
Hmel2/annotation/._Hmel2_proteins.fa
Hmel2/annotation/Hmel2_proteins.fa
Hmel2/annotation/._Hmel_mtDNA.gff
Hmel2/annotation/Hmel_mtDNA.gff

Prereqs - Install ipyrad

Full install details for all platforms are here: http://ipyrad.readthedocs.io/installation.html

In [69]:
%%bash -s "$WORK_DIR"
## Must always export the new miniconda path in each bash cell. We do this
## so the analysis pipeline is totally self contained, it doesn't read to
## or write from anywwhere but the WORK_DIR.
## There's probably a magic way to do this but i can't figure it out
export PATH="$1/miniconda/bin:$PATH"; export "WORK_DIR=$1"

## Fetch the latest miniconda installer
wget --quiet https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh

## Install miniconda silently to the work directory.
## -b means "batch" mode, -f is force overwrite and -p is the install dir
bash Miniconda-latest-Linux-x86_64.sh -b -f -p $WORK_DIR/miniconda

conda update -y conda                 ## updates conda
conda install -y -c ipyrad ipyrad     ## installs the latest release (silently `-y`)
/home/iovercast/manuscript-analysis//miniconda/bin:/home/iovercast/opt/miniconda/bin:/home/iovercast/opt/bin:/cm/shared/apps/slurm/14.11.6/sbin:/cm/shared/apps/slurm/14.11.6/bin:/cm/local/apps/gcc/5.1.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/sbin:/home/iovercast/.local/bin:/home/iovercast/bin
PREFIX=/home/iovercast/manuscript-analysis/miniconda
installing: _cache-0.0-py27_x0 ...
installing: python-2.7.11-0 ...
installing: conda-env-2.4.5-py27_0 ...
installing: openssl-1.0.2g-0 ...
installing: pycosat-0.6.1-py27_0 ...
installing: pyyaml-3.11-py27_1 ...
installing: readline-6.2-2 ...
installing: requests-2.9.1-py27_0 ...
installing: sqlite-3.9.2-0 ...
installing: tk-8.5.18-0 ...
installing: yaml-0.1.6-0 ...
installing: zlib-1.2.8-0 ...
installing: conda-4.0.5-py27_0 ...
installing: pycrypto-2.6.1-py27_0 ...
installing: pip-8.1.1-py27_1 ...
installing: wheel-0.29.0-py27_0 ...
installing: setuptools-20.3-py27_0 ...
creating default environment...
installation finished.
Fetching package metadata: ....
.Solving package specifications: .........

Package plan for installation in environment /home/iovercast/manuscript-analysis/miniconda:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    sqlite-3.13.0              |                0         4.0 MB
    python-2.7.12              |                1        12.1 MB
    conda-env-2.5.1            |           py27_0          26 KB
    ruamel_yaml-0.11.14        |           py27_0         352 KB
    conda-4.1.11               |           py27_0         201 KB
    ------------------------------------------------------------
                                           Total:        16.6 MB

The following NEW packages will be INSTALLED:

    ruamel_yaml: 0.11.14-py27_0

The following packages will be UPDATED:

    conda:       4.0.5-py27_0 --> 4.1.11-py27_0 
    conda-env:   2.4.5-py27_0 --> 2.5.1-py27_0  
    python:      2.7.11-0     --> 2.7.12-1      
    sqlite:      3.9.2-0      --> 3.13.0-0      

Fetching packages ...
sqlite-3.13.0- 100% |###############################| Time: 0:00:00  13.28 MB/s
python-2.7.12- 100% |###############################| Time: 0:00:00  20.08 MB/s
conda-env-2.5. 100% |###############################| Time: 0:00:00   2.12 MB/s
ruamel_yaml-0. 100% |###############################| Time: 0:00:00   4.33 MB/s
conda-4.1.11-p 100% |###############################| Time: 0:00:00   3.09 MB/s
Extracting packages ...
[      COMPLETE      ]|##################################################| 100%
Unlinking packages ...
[      COMPLETE      ]|##################################################| 100%
Linking packages ...
[      COMPLETE      ]|##################################################| 100%
Fetching package metadata .........
Solving package specifications: ..........

Package plan for installation in environment /home/iovercast/manuscript-analysis/miniconda:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    libffi-3.2.1               |                0          36 KB
    libgfortran-3.0.0          |                1         281 KB
    libsodium-1.0.10           |                0         1.2 MB
    mkl-11.3.3                 |                0       122.1 MB
    mpich2-1.4.1p1             |                0         2.6 MB
    pixman-0.32.6              |                0         2.4 MB
    glib-2.43.0                |                1         5.4 MB
    hdf5-1.8.17                |                1         1.9 MB
    libpng-1.6.22              |                0         214 KB
    libxml2-2.9.2              |                0         4.2 MB
    zeromq-4.1.4               |                0         4.1 MB
    alabaster-0.7.8            |           py27_0          18 KB
    backports-1.0              |           py27_0           1 KB
    backports_abc-0.4          |           py27_0           5 KB
    conda-env-2.5.2            |           py27_0          26 KB
    cython-0.24.1              |           py27_0         5.3 MB
    decorator-4.0.10           |           py27_0          12 KB
    docutils-0.12              |           py27_2         637 KB
    enum34-1.1.6               |           py27_0          53 KB
    freetype-2.5.5             |                1         2.5 MB
    funcsigs-1.0.2             |           py27_0          18 KB
    functools32-3.2.3.2        |           py27_0          15 KB
    futures-3.0.5              |           py27_0          18 KB
    imagesize-0.7.1            |           py27_0           3 KB
    ipython_genutils-0.1.0     |           py27_0          32 KB
    markupsafe-0.23            |           py27_2          31 KB
    mistune-0.7.2              |           py27_0         570 KB
    mpi4py-2.0.0               |           py27_1         1.7 MB
    numpy-1.11.1               |           py27_0         6.2 MB
    path.py-8.2.1              |           py27_0          45 KB
    ptyprocess-0.5.1           |           py27_0          19 KB
    pygments-2.1.3             |           py27_0         1.2 MB
    pytz-2016.6.1              |           py27_0         178 KB
    pyzmq-15.4.0               |           py27_0         705 KB
    simplegeneric-0.8.1        |           py27_1           7 KB
    sip-4.18                   |           py27_0         264 KB
    six-1.10.0                 |           py27_0          16 KB
    snowballstemmer-1.2.1      |           py27_0          73 KB
    sphinx_rtd_theme-0.1.9     |           py27_0         628 KB
    wcwidth-0.1.7              |           py27_0          21 KB
    babel-2.3.3                |           py27_0         4.9 MB
    clyent-1.2.2               |           py27_0          15 KB
    configparser-3.5.0         |           py27_0          31 KB
    fontconfig-2.11.1          |                6         405 KB
    get_terminal_size-1.0.0    |           py27_0           4 KB
    h5py-2.6.0                 |      np111py27_2         2.4 MB
    jinja2-2.8                 |           py27_1         264 KB
    jsonschema-2.5.1           |           py27_0          55 KB
    llvmlite-0.13.0            |           py27_0         7.5 MB
    pathlib2-2.1.0             |           py27_0          26 KB
    pexpect-4.0.1              |           py27_0          63 KB
    prompt_toolkit-1.0.3       |           py27_0         295 KB
    python-dateutil-2.5.3      |           py27_0         236 KB
    scipy-0.18.0               |      np111py27_0        31.0 MB
    singledispatch-3.4.0.3     |           py27_0          12 KB
    ssl_match_hostname-3.4.0.2 |           py27_1           6 KB
    traitlets-4.2.2            |           py27_0         108 KB
    anaconda-client-1.5.1      |           py27_0         110 KB
    cairo-1.12.18              |                6         594 KB
    entrypoints-0.2.2          |           py27_0           6 KB
    jupyter_core-4.1.1         |           py27_0          51 KB
    numba-0.28.1               |      np111py27_0         2.1 MB
    pandas-0.18.1              |      np111py27_0        13.0 MB
    pickleshare-0.7.3          |           py27_0           8 KB
    sphinx-1.4.1               |           py27_0         1.2 MB
    tornado-4.4.1              |           py27_0         552 KB
    harfbuzz-0.9.39            |                1         1.1 MB
    ipython-5.1.0              |           py27_0         936 KB
    jupyter_client-4.3.0       |           py27_0          96 KB
    nbformat-4.1.0             |           py27_0         115 KB
    terminado-0.6              |           py27_0          18 KB
    ipykernel-4.4.1            |           py27_0         122 KB
    nbconvert-4.2.0            |           py27_0         310 KB
    pango-1.39.0               |                1         668 KB
    ipyparallel-5.2.0          |           py27_0         267 KB
    jupyter_console-5.0.0      |           py27_0          28 KB
    notebook-4.2.2             |           py27_0         5.0 MB
    qt-4.8.7                   |                4        32.7 MB
    pyqt-4.11.4                |           py27_4         3.3 MB
    widgetsnbextension-1.2.6   |           py27_0         1.1 MB
    qtconsole-4.2.1            |           py27_0         159 KB
    ipyrad-0.3.36              |                4        16.6 MB  ipyrad
    ipywidgets-5.2.2           |           py27_0          58 KB
    jupyter-1.0.0              |           py27_3           3 KB
    nb_anacondacloud-1.2.0     |           py27_0          23 KB
    nb_conda_kernels-2.0.0     |           py27_0          30 KB
    nb_conda-2.0.0             |           py27_0          28 KB
    _nb_ext_conf-0.3.0         |           py27_0          956 B
    nbpresent-3.0.2            |           py27_0         463 KB
    ------------------------------------------------------------
                                           Total:       292.5 MB

The following NEW packages will be INSTALLED:

    _nb_ext_conf:       0.3.0-py27_0             
    alabaster:          0.7.8-py27_0             
    anaconda-client:    1.5.1-py27_0             
    babel:              2.3.3-py27_0             
    backports:          1.0-py27_0               
    backports_abc:      0.4-py27_0               
    cairo:              1.12.18-6                
    clyent:             1.2.2-py27_0             
    configparser:       3.5.0-py27_0             
    cython:             0.24.1-py27_0            
    decorator:          4.0.10-py27_0            
    docutils:           0.12-py27_2              
    entrypoints:        0.2.2-py27_0             
    enum34:             1.1.6-py27_0             
    fontconfig:         2.11.1-6                 
    freetype:           2.5.5-1                  
    funcsigs:           1.0.2-py27_0             
    functools32:        3.2.3.2-py27_0           
    futures:            3.0.5-py27_0             
    get_terminal_size:  1.0.0-py27_0             
    glib:               2.43.0-1                 
    h5py:               2.6.0-np111py27_2        
    harfbuzz:           0.9.39-1                 
    hdf5:               1.8.17-1                 
    imagesize:          0.7.1-py27_0             
    ipykernel:          4.4.1-py27_0             
    ipyparallel:        5.2.0-py27_0             
    ipyrad:             0.3.36-4           ipyrad
    ipython:            5.1.0-py27_0             
    ipython_genutils:   0.1.0-py27_0             
    ipywidgets:         5.2.2-py27_0             
    jinja2:             2.8-py27_1               
    jsonschema:         2.5.1-py27_0             
    jupyter:            1.0.0-py27_3             
    jupyter_client:     4.3.0-py27_0             
    jupyter_console:    5.0.0-py27_0             
    jupyter_core:       4.1.1-py27_0             
    libffi:             3.2.1-0                  
    libgfortran:        3.0.0-1                  
    libpng:             1.6.22-0                 
    libsodium:          1.0.10-0                 
    libxml2:            2.9.2-0                  
    llvmlite:           0.13.0-py27_0            
    markupsafe:         0.23-py27_2              
    mistune:            0.7.2-py27_0             
    mkl:                11.3.3-0                 
    mpi4py:             2.0.0-py27_1             
    mpich2:             1.4.1p1-0                
    nb_anacondacloud:   1.2.0-py27_0             
    nb_conda:           2.0.0-py27_0             
    nb_conda_kernels:   2.0.0-py27_0             
    nbconvert:          4.2.0-py27_0             
    nbformat:           4.1.0-py27_0             
    nbpresent:          3.0.2-py27_0             
    notebook:           4.2.2-py27_0             
    numba:              0.28.1-np111py27_0       
    numpy:              1.11.1-py27_0            
    pandas:             0.18.1-np111py27_0       
    pango:              1.39.0-1                 
    path.py:            8.2.1-py27_0             
    pathlib2:           2.1.0-py27_0             
    pexpect:            4.0.1-py27_0             
    pickleshare:        0.7.3-py27_0             
    pixman:             0.32.6-0                 
    prompt_toolkit:     1.0.3-py27_0             
    ptyprocess:         0.5.1-py27_0             
    pygments:           2.1.3-py27_0             
    pyqt:               4.11.4-py27_4            
    python-dateutil:    2.5.3-py27_0             
    pytz:               2016.6.1-py27_0          
    pyzmq:              15.4.0-py27_0            
    qt:                 4.8.7-4                  
    qtconsole:          4.2.1-py27_0             
    scipy:              0.18.0-np111py27_0       
    simplegeneric:      0.8.1-py27_1             
    singledispatch:     3.4.0.3-py27_0           
    sip:                4.18-py27_0              
    six:                1.10.0-py27_0            
    snowballstemmer:    1.2.1-py27_0             
    sphinx:             1.4.1-py27_0             
    sphinx_rtd_theme:   0.1.9-py27_0             
    ssl_match_hostname: 3.4.0.2-py27_1           
    terminado:          0.6-py27_0               
    tornado:            4.4.1-py27_0             
    traitlets:          4.2.2-py27_0             
    wcwidth:            0.1.7-py27_0             
    widgetsnbextension: 1.2.6-py27_0             
    zeromq:             4.1.4-0                  

The following packages will be UPDATED:

    conda-env:          2.5.1-py27_0              --> 2.5.2-py27_0

Fetching packages ...
libffi-3.2.1-0 100% |###############################| Time: 0:00:00   1.68 MB/s
libgfortran-3. 100% |###############################| Time: 0:00:00   3.63 MB/s
libsodium-1.0. 100% |###############################| Time: 0:00:00   8.45 MB/s
mkl-11.3.3-0.t 100% |###############################| Time: 0:00:04  26.16 MB/s
mpich2-1.4.1p1 100% |###############################| Time: 0:00:00  14.88 MB/s
pixman-0.32.6- 100% |###############################| Time: 0:00:00  12.81 MB/s
glib-2.43.0-1. 100% |###############################| Time: 0:00:00  17.50 MB/s
hdf5-1.8.17-1. 100% |###############################| Time: 0:00:00  11.96 MB/s
libpng-1.6.22- 100% |###############################| Time: 0:00:00   3.29 MB/s
libxml2-2.9.2- 100% |###############################| Time: 0:00:00  16.92 MB/s
zeromq-4.1.4-0 100% |###############################| Time: 0:00:00  16.64 MB/s
alabaster-0.7. 100% |###############################| Time: 0:00:00   1.41 MB/s
backports-1.0- 100% |###############################| Time: 0:00:00 967.72 kB/s
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Python 2.7.11 :: Continuum Analytics, Inc.
In [70]:
%%bash -s "$WORK_DIR"
export PATH="$1/miniconda/bin:$PATH"
which ipyrad
/home/iovercast/manuscript-analysis/miniconda/bin/ipyrad

Prereqs - Install pyrad

In [71]:
%%bash -s "$WORK_DIR"
export PATH="$1/miniconda/bin:$PATH"; export "WORK_DIR=$1"

## Fetch and install prerequisites. This takes a few minutes so be patient

## Should be unnecessary because numpy and scipy already installed by conda
conda install numpy scipy
wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
tar -xvzf muscle*.tar.gz

## This unpacks the muscle binary in the current working directory
## You can test it to see if it runs:
./muscle3.8.31_i86linux64 -h

## Copy to miniconda/bin so it will be in your path
## Maybe not technically 'correct' but it'll work for our purposes
cp muscle3.8.31_i86linux64 $WORK_DIR/miniconda/bin/muscle

## Download and install vsearch
wget https://github.com/torognes/vsearch/releases/download/v2.0.3/vsearch-2.0.3-linux-x86_64.tar.gz
tar xzf vsearch-2.0.3-linux-x86_64.tar.gz
cp vsearch-2.0.3-linux-x86_64/bin/vsearch $WORK_DIR/miniconda/bin/vsearch

## Fetch pyrad source from the git repository
git clone https://github.com/dereneaton/pyrad.git
cd pyrad

## If you are using anaconda you can simply run setup.py to
## install pyrad into your conda environment
python setup.py install

which muscle
which vsearch
which pyrad
Fetching package metadata .......
Solving package specifications: ..........

# All requested packages already installed.
# packages in environment at /home/iovercast/manuscript-analysis/miniconda:
#
numpy                     1.11.1                   py27_0  
scipy                     0.18.0              np111py27_0  
muscle3.8.31_i86linux64
running install
running bdist_egg
running egg_info
creating pyrad.egg-info
writing requirements to pyrad.egg-info/requires.txt
writing pyrad.egg-info/PKG-INFO
writing top-level names to pyrad.egg-info/top_level.txt
writing dependency_links to pyrad.egg-info/dependency_links.txt
writing entry points to pyrad.egg-info/entry_points.txt
writing manifest file 'pyrad.egg-info/SOURCES.txt'
reading manifest file 'pyrad.egg-info/SOURCES.txt'
writing manifest file 'pyrad.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
creating build
creating build/lib
creating build/lib/pyrad
copying pyrad/Dtest.py -> build/lib/pyrad
copying pyrad/Dtest_5.py -> build/lib/pyrad
copying pyrad/Dtest_foil.py -> build/lib/pyrad
copying pyrad/H_err_dp.py -> build/lib/pyrad
copying pyrad/__init__.py -> build/lib/pyrad
copying pyrad/alignable.py -> build/lib/pyrad
copying pyrad/cluster7dp.py -> build/lib/pyrad
copying pyrad/cluster_cons7_shuf.py -> build/lib/pyrad
copying pyrad/consens_pairs.py -> build/lib/pyrad
copying pyrad/consensdp.py -> build/lib/pyrad
copying pyrad/createfile.py -> build/lib/pyrad
copying pyrad/editraw_merges.py -> build/lib/pyrad
copying pyrad/editraw_pairs.py -> build/lib/pyrad
copying pyrad/editraw_rads.py -> build/lib/pyrad
copying pyrad/loci2SNP.py -> build/lib/pyrad
copying pyrad/loci2gphocs.py -> build/lib/pyrad
copying pyrad/loci2mig.py -> build/lib/pyrad
copying pyrad/loci2phynex.py -> build/lib/pyrad
copying pyrad/loci2treemix.py -> build/lib/pyrad
copying pyrad/loci2vcf.py -> build/lib/pyrad
copying pyrad/overlapcheck.py -> build/lib/pyrad
copying pyrad/potpour.py -> build/lib/pyrad
copying pyrad/pyRAD.py -> build/lib/pyrad
copying pyrad/sortandcheck2.py -> build/lib/pyrad
copying pyrad/tier2clust.py -> build/lib/pyrad
creating build/bdist.linux-x86_64
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/Dtest.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/Dtest_5.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/Dtest_foil.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/H_err_dp.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/__init__.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/alignable.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/cluster7dp.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/cluster_cons7_shuf.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/consens_pairs.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/consensdp.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/createfile.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/editraw_merges.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/editraw_pairs.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/editraw_rads.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/loci2SNP.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/loci2gphocs.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/loci2mig.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/loci2phynex.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/loci2treemix.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/loci2vcf.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/overlapcheck.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/potpour.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/pyRAD.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/sortandcheck2.py -> build/bdist.linux-x86_64/egg/pyrad
copying build/lib/pyrad/tier2clust.py -> build/bdist.linux-x86_64/egg/pyrad
byte-compiling build/bdist.linux-x86_64/egg/pyrad/Dtest.py to Dtest.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/Dtest_5.py to Dtest_5.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/Dtest_foil.py to Dtest_foil.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/H_err_dp.py to H_err_dp.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/alignable.py to alignable.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/cluster7dp.py to cluster7dp.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/cluster_cons7_shuf.py to cluster_cons7_shuf.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/consens_pairs.py to consens_pairs.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/consensdp.py to consensdp.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/createfile.py to createfile.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/editraw_merges.py to editraw_merges.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/editraw_pairs.py to editraw_pairs.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/editraw_rads.py to editraw_rads.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/loci2SNP.py to loci2SNP.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/loci2gphocs.py to loci2gphocs.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/loci2mig.py to loci2mig.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/loci2phynex.py to loci2phynex.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/loci2treemix.py to loci2treemix.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/loci2vcf.py to loci2vcf.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/overlapcheck.py to overlapcheck.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/potpour.py to potpour.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/pyRAD.py to pyRAD.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/sortandcheck2.py to sortandcheck2.pyc
byte-compiling build/bdist.linux-x86_64/egg/pyrad/tier2clust.py to tier2clust.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
copying pyrad.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyrad.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyrad.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyrad.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyrad.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying pyrad.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating dist
creating 'dist/pyrad-3.0.66-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing pyrad-3.0.66-py2.7.egg
Copying pyrad-3.0.66-py2.7.egg to /home/iovercast/manuscript-analysis/miniconda/lib/python2.7/site-packages
Adding pyrad 3.0.66 to easy-install.pth file
Installing pyrad script to /home/iovercast/manuscript-analysis/miniconda/bin

Installed /home/iovercast/manuscript-analysis/miniconda/lib/python2.7/site-packages/pyrad-3.0.66-py2.7.egg
Processing dependencies for pyrad==3.0.66
Searching for scipy==0.18.0
Best match: scipy 0.18.0
Adding scipy 0.18.0 to easy-install.pth file

Using /home/iovercast/manuscript-analysis/miniconda/lib/python2.7/site-packages
Searching for numpy==1.11.1
Best match: numpy 1.11.1
Adding numpy 1.11.1 to easy-install.pth file

Using /home/iovercast/manuscript-analysis/miniconda/lib/python2.7/site-packages
Finished processing dependencies for pyrad==3.0.66
/home/iovercast/manuscript-analysis/miniconda/bin/muscle
/home/iovercast/manuscript-analysis/miniconda/bin/vsearch
/home/iovercast/manuscript-analysis/miniconda/bin/pyrad
Using Anaconda API: https://api.anaconda.org
--2016-09-01 17:05:22--  http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
Resolving www.drive5.com (www.drive5.com)... 199.195.116.69
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Invalid command line option "h"

MUSCLE v3.8.31 by Robert C. Edgar

http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.


Basic usage

    muscle -in <inputfile> -out <outputfile>

Common options (for a complete list please see the User Guide):

    -in <inputfile>    Input file in FASTA format (default stdin)
    -out <outputfile>  Output alignment in FASTA format (default stdout)
    -diags             Find diagonals (faster for similar sequences)
    -maxiters <n>      Maximum number of iterations (integer, default 16)
    -maxhours <h>      Maximum time to iterate in hours (default no limit)
    -html              Write output in HTML format (default FASTA)
    -msf               Write output in GCG MSF format (default FASTA)
    -clw               Write output in CLUSTALW format (default FASTA)
    -clwstrict         As -clw, with 'CLUSTAL W (1.81)' header
    -log[a] <logfile>  Log to file (append if -loga, overwrite if -log)
    -quiet             Do not write progress messages to stderr
    -version           Display version information and exit

Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
Fastest possible (nucleotides): -maxiters 1 -diags
--2016-09-01 17:05:23--  https://github.com/torognes/vsearch/releases/download/v2.0.3/vsearch-2.0.3-linux-x86_64.tar.gz
Resolving github.com (github.com)... 192.30.253.112
Connecting to github.com (github.com)|192.30.253.112|:443... connected.
HTTP request sent, awaiting response... 302 Found
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Resolving github-cloud.s3.amazonaws.com (github-cloud.s3.amazonaws.com)... 54.231.40.51
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   100K .......... .......... .......... .......... .......... 31% 1.34M 0s
   150K .......... .......... .......... .......... .......... 42% 1.32M 0s
   200K .......... .......... .......... .......... .......... 52% 1.79M 0s
   250K .......... .......... .......... .......... .......... 63% 1.40M 0s
   300K .......... .......... .......... .......... .......... 73% 1.76M 0s
   350K .......... .......... .......... .......... .......... 84% 2.41M 0s
   400K .......... .......... .......... .......... .......... 94% 1.86M 0s
   450K .......... .......... ......                          100% 2.86M=0.3s

2016-09-01 17:05:24 (1.54 MB/s) - ‘vsearch-2.0.3-linux-x86_64.tar.gz’ saved [487583/487583]

Cloning into 'pyrad'...
zip_safe flag not set; analyzing archive contents...

Prereqs - Download and install stacks

NB: Stacks is trickier to build on OSX, I had to compile it on a different machine and then scp the binaries to the box I was working on.

Stacks is picky about where stuff installs to. If you don't have permission to install to /usr/local (most HPC systems) then you need to provide the --prefix argument to ./configure

In [74]:
%%bash -s "$WORK_DIR"
export PATH="$1/miniconda/bin:$PATH"; export "WORK_DIR=$1"
cd $WORK_DIR

## 1.42 is the version that crashed during cstacks on the simdata. Julian fixed
## the bug and pushed 1.43 which seems to work great.
#wget http://catchenlab.life.illinois.edu/stacks/source/stacks-1.42.tar.gz
wget http://catchenlab.life.illinois.edu/stacks/source/stacks-1.43.tar.gz
tar -xvzf stacks-1.43.tar.gz
cd stacks-1.43
./configure --prefix=$WORK_DIR/miniconda
make
make install

cd $WORK_DIR
which process_radtags
stacks-1.42/
stacks-1.42/acinclude.m4
stacks-1.42/aclocal.m4
stacks-1.42/autogen.sh
stacks-1.42/ChangeLog
stacks-1.42/config/
stacks-1.42/config.h.in
stacks-1.42/configure
stacks-1.42/configure.ac
stacks-1.42/htslib/
stacks-1.42/INSTALL
stacks-1.42/LICENSE
stacks-1.42/Makefile.am
stacks-1.42/Makefile.in
stacks-1.42/php/
stacks-1.42/README
stacks-1.42/scripts/
stacks-1.42/sql/
stacks-1.42/src/
stacks-1.42/tests/
stacks-1.42/tests/kmer_filter.t
stacks-1.42/tests/process_radtags.t
stacks-1.42/tests/pstacks.t
stacks-1.42/tests/ustacks.t
stacks-1.42/src/aln_utils.cc
stacks-1.42/src/aln_utils.h
stacks-1.42/src/BamI.h
stacks-1.42/src/BamUnalignedI.h
stacks-1.42/src/bootstrap.h
stacks-1.42/src/BowtieI.h
stacks-1.42/src/BustardI.h
stacks-1.42/src/catalog_utils.cc
stacks-1.42/src/catalog_utils.h
stacks-1.42/src/clean.cc
stacks-1.42/src/clean.h
stacks-1.42/src/clone_filter.cc
stacks-1.42/src/clone_filter.h
stacks-1.42/src/cmb.cc
stacks-1.42/src/cmb.h
stacks-1.42/src/constants.h
stacks-1.42/src/cstacks.cc
stacks-1.42/src/cstacks.h
stacks-1.42/src/DNANSeq.cc
stacks-1.42/src/DNANSeq.h
stacks-1.42/src/DNASeq.cc
stacks-1.42/src/DNASeq.h
stacks-1.42/src/estacks.cc
stacks-1.42/src/estacks.h
stacks-1.42/src/export_formats.cc
stacks-1.42/src/export_formats.h
stacks-1.42/src/FastaI.h
stacks-1.42/src/FastqI.h
stacks-1.42/src/file_io.cc
stacks-1.42/src/file_io.h
stacks-1.42/src/GappedAln.h
stacks-1.42/src/genotype_dictionaries.cc
stacks-1.42/src/genotype_dictionaries.h
stacks-1.42/src/genotypes.cc
stacks-1.42/src/genotypes.h
stacks-1.42/src/gzFasta.h
stacks-1.42/src/gzFastq.h
stacks-1.42/src/hstacks.cc
stacks-1.42/src/hstacks.h
stacks-1.42/src/input.cc
stacks-1.42/src/input.h
stacks-1.42/src/kmer_filter.cc
stacks-1.42/src/kmer_filter.h
stacks-1.42/src/kmers.cc
stacks-1.42/src/kmers.h
stacks-1.42/src/locus.cc
stacks-1.42/src/locus.h
stacks-1.42/src/log_utils.cc
stacks-1.42/src/log_utils.h
stacks-1.42/src/MetaPopInfo.cc
stacks-1.42/src/MetaPopInfo.h
stacks-1.42/src/models.cc
stacks-1.42/src/models.h
stacks-1.42/src/mst.cc
stacks-1.42/src/mst.h
stacks-1.42/src/mstack.cc
stacks-1.42/src/mstack.h
stacks-1.42/src/ordered.h
stacks-1.42/src/phasedstacks.cc
stacks-1.42/src/phasedstacks.h
stacks-1.42/src/PopMap.h
stacks-1.42/src/PopSum.h
stacks-1.42/src/populations.cc
stacks-1.42/src/populations.h
stacks-1.42/src/process_radtags.cc
stacks-1.42/src/process_radtags.h
stacks-1.42/src/process_shortreads.cc
stacks-1.42/src/process_shortreads.h
stacks-1.42/src/pstacks.cc
stacks-1.42/src/pstacks.h
stacks-1.42/src/renz.cc
stacks-1.42/src/renz.h
stacks-1.42/src/rxstacks.cc
stacks-1.42/src/rxstacks.h
stacks-1.42/src/SamI.h
stacks-1.42/src/smoothing.h
stacks-1.42/src/smoothing_utils.h
stacks-1.42/src/sql_utilities.cc
stacks-1.42/src/sql_utilities.h
stacks-1.42/src/sstacks.cc
stacks-1.42/src/sstacks.h
stacks-1.42/src/stacks.cc
stacks-1.42/src/stacks.h
stacks-1.42/src/Tsv.h
stacks-1.42/src/ustacks.cc
stacks-1.42/src/ustacks.h
stacks-1.42/src/utils.cc
stacks-1.42/src/utils.h
stacks-1.42/src/Vcf.cc
stacks-1.42/src/Vcf.h
stacks-1.42/src/write.cc
stacks-1.42/src/write.h
stacks-1.42/sql/catalog_index.sql
stacks-1.42/sql/chr_index.sql
stacks-1.42/sql/mysql.cnf.dist
stacks-1.42/sql/stacks.sql
stacks-1.42/sql/tag_index.sql
stacks-1.42/scripts/convert_stacks.pl
stacks-1.42/scripts/denovo_map.pl
stacks-1.42/scripts/exec_velvet.pl
stacks-1.42/scripts/export_sql.pl
stacks-1.42/scripts/extract_interpop_chars.pl
stacks-1.42/scripts/index_radtags.pl
stacks-1.42/scripts/integrate_alignments.py
stacks-1.42/scripts/load_radtags.pl
stacks-1.42/scripts/load_sequences.pl
stacks-1.42/scripts/ref_map.pl
stacks-1.42/scripts/sort_read_pairs.pl
stacks-1.42/scripts/stacks_export_notify.pl
stacks-1.42/php/ajax.js
stacks-1.42/php/annotate.js
stacks-1.42/php/annotate_marker.php
stacks-1.42/php/catalog.php
stacks-1.42/php/catalog_genotypes.php
stacks-1.42/php/CatalogClass.php
stacks-1.42/php/constants.php.dist
stacks-1.42/php/correct_genotype.php
stacks-1.42/php/correct_genotypes.php
stacks-1.42/php/db_functions.php
stacks-1.42/php/export.js
stacks-1.42/php/export_batch.php
stacks-1.42/php/fst_view.php
stacks-1.42/php/hapstat_view.php
stacks-1.42/php/header.php
stacks-1.42/php/images/
stacks-1.42/php/index.php
stacks-1.42/php/last_modified.php
stacks-1.42/php/Locus.php
stacks-1.42/php/phist_view.php
stacks-1.42/php/pop_view.php
stacks-1.42/php/population_view.js
stacks-1.42/php/samples.php
stacks-1.42/php/sequence_blast.php
stacks-1.42/php/stack_view.php
stacks-1.42/php/stacks.css
stacks-1.42/php/stacks.js
stacks-1.42/php/stacks_functions.php
stacks-1.42/php/sumstat_view.php
stacks-1.42/php/tag.php
stacks-1.42/php/tags.php
stacks-1.42/php/version.php
stacks-1.42/php/view_sequence.php
stacks-1.42/php/images/caret-d.png
stacks-1.42/php/images/caret-u.png
stacks-1.42/php/images/excel_icon.png
stacks-1.42/php/images/l-arrow-disabled.png
stacks-1.42/php/images/l-arrow.png
stacks-1.42/php/images/r-arrow-disabled.png
stacks-1.42/php/images/r-arrow.png
stacks-1.42/php/images/stacks_bg.png
stacks-1.42/php/images/stacks_logo_rev_small.png
stacks-1.42/htslib/._bgzf.c
stacks-1.42/htslib/bgzf.c
stacks-1.42/htslib/._bgzip.c
stacks-1.42/htslib/bgzip.c
stacks-1.42/htslib/._cram
stacks-1.42/htslib/cram/
stacks-1.42/htslib/._faidx.c
stacks-1.42/htslib/faidx.c
stacks-1.42/htslib/._hfile.c
stacks-1.42/htslib/hfile.c
stacks-1.42/htslib/._hfile_internal.h
stacks-1.42/htslib/hfile_internal.h
stacks-1.42/htslib/._hfile_irods.c
stacks-1.42/htslib/hfile_irods.c
stacks-1.42/htslib/._hfile_libcurl.c
stacks-1.42/htslib/hfile_libcurl.c
stacks-1.42/htslib/._hfile_net.c
stacks-1.42/htslib/hfile_net.c
stacks-1.42/htslib/._hts.c
stacks-1.42/htslib/hts.c
stacks-1.42/htslib/._hts_internal.h
stacks-1.42/htslib/hts_internal.h
stacks-1.42/htslib/._htsfile.c
stacks-1.42/htslib/htsfile.c
stacks-1.42/htslib/._htslib
stacks-1.42/htslib/htslib/
stacks-1.42/htslib/._htslib.pc.in
stacks-1.42/htslib/htslib.pc.in
stacks-1.42/htslib/._htslib_vars.mk
stacks-1.42/htslib/htslib_vars.mk
stacks-1.42/htslib/._INSTALL
stacks-1.42/htslib/INSTALL
stacks-1.42/htslib/._kfunc.c
stacks-1.42/htslib/kfunc.c
stacks-1.42/htslib/._knetfile.c
stacks-1.42/htslib/knetfile.c
stacks-1.42/htslib/._kstring.c
stacks-1.42/htslib/kstring.c
stacks-1.42/htslib/._LICENSE
stacks-1.42/htslib/LICENSE
stacks-1.42/htslib/._Makefile
stacks-1.42/htslib/Makefile
stacks-1.42/htslib/._md5.c
stacks-1.42/htslib/md5.c
stacks-1.42/htslib/._NEWS
stacks-1.42/htslib/NEWS
stacks-1.42/htslib/._plugin.c
stacks-1.42/htslib/plugin.c
stacks-1.42/htslib/._README
stacks-1.42/htslib/README
stacks-1.42/htslib/._regidx.c
stacks-1.42/htslib/regidx.c
stacks-1.42/htslib/._sam.c
stacks-1.42/htslib/sam.c
stacks-1.42/htslib/._synced_bcf_reader.c
stacks-1.42/htslib/synced_bcf_reader.c
stacks-1.42/htslib/._tabix.c
stacks-1.42/htslib/tabix.c
stacks-1.42/htslib/._tbx.c
stacks-1.42/htslib/tbx.c
stacks-1.42/htslib/._vcf.c
stacks-1.42/htslib/vcf.c
stacks-1.42/htslib/._vcf_sweep.c
stacks-1.42/htslib/vcf_sweep.c
stacks-1.42/htslib/._vcfutils.c
stacks-1.42/htslib/vcfutils.c
stacks-1.42/htslib/htslib/._bgzf.h
stacks-1.42/htslib/htslib/bgzf.h
stacks-1.42/htslib/htslib/._cram.h
stacks-1.42/htslib/htslib/cram.h
stacks-1.42/htslib/htslib/._faidx.h
stacks-1.42/htslib/htslib/faidx.h
stacks-1.42/htslib/htslib/._hfile.h
stacks-1.42/htslib/htslib/hfile.h
stacks-1.42/htslib/htslib/._hts.h
stacks-1.42/htslib/htslib/hts.h
stacks-1.42/htslib/htslib/._hts_defs.h
stacks-1.42/htslib/htslib/hts_defs.h
stacks-1.42/htslib/htslib/._kbitset.h
stacks-1.42/htslib/htslib/kbitset.h
stacks-1.42/htslib/htslib/._kfunc.h
stacks-1.42/htslib/htslib/kfunc.h
stacks-1.42/htslib/htslib/._khash.h
stacks-1.42/htslib/htslib/khash.h
stacks-1.42/htslib/htslib/._khash_str2int.h
stacks-1.42/htslib/htslib/khash_str2int.h
stacks-1.42/htslib/htslib/._klist.h
stacks-1.42/htslib/htslib/klist.h
stacks-1.42/htslib/htslib/._knetfile.h
stacks-1.42/htslib/htslib/knetfile.h
stacks-1.42/htslib/htslib/._kseq.h
stacks-1.42/htslib/htslib/kseq.h
stacks-1.42/htslib/htslib/._ksort.h
stacks-1.42/htslib/htslib/ksort.h
stacks-1.42/htslib/htslib/._kstring.h
stacks-1.42/htslib/htslib/kstring.h
stacks-1.42/htslib/htslib/._regidx.h
stacks-1.42/htslib/htslib/regidx.h
stacks-1.42/htslib/htslib/._sam.h
stacks-1.42/htslib/htslib/sam.h
stacks-1.42/htslib/htslib/._synced_bcf_reader.h
stacks-1.42/htslib/htslib/synced_bcf_reader.h
stacks-1.42/htslib/htslib/._tbx.h
stacks-1.42/htslib/htslib/tbx.h
stacks-1.42/htslib/htslib/._vcf.h
stacks-1.42/htslib/htslib/vcf.h
stacks-1.42/htslib/htslib/._vcf_sweep.h
stacks-1.42/htslib/htslib/vcf_sweep.h
stacks-1.42/htslib/htslib/._vcfutils.h
stacks-1.42/htslib/htslib/vcfutils.h
stacks-1.42/htslib/cram/._cram.h
stacks-1.42/htslib/cram/cram.h
stacks-1.42/htslib/cram/._cram_codecs.c
stacks-1.42/htslib/cram/cram_codecs.c
stacks-1.42/htslib/cram/._cram_codecs.h
stacks-1.42/htslib/cram/cram_codecs.h
stacks-1.42/htslib/cram/._cram_decode.c
stacks-1.42/htslib/cram/cram_decode.c
stacks-1.42/htslib/cram/._cram_decode.h
stacks-1.42/htslib/cram/cram_decode.h
stacks-1.42/htslib/cram/._cram_encode.c
stacks-1.42/htslib/cram/cram_encode.c
stacks-1.42/htslib/cram/._cram_encode.h
stacks-1.42/htslib/cram/cram_encode.h
stacks-1.42/htslib/cram/._cram_external.c
stacks-1.42/htslib/cram/cram_external.c
stacks-1.42/htslib/cram/._cram_index.c
stacks-1.42/htslib/cram/cram_index.c
stacks-1.42/htslib/cram/._cram_index.h
stacks-1.42/htslib/cram/cram_index.h
stacks-1.42/htslib/cram/._cram_io.c
stacks-1.42/htslib/cram/cram_io.c
stacks-1.42/htslib/cram/._cram_io.h
stacks-1.42/htslib/cram/cram_io.h
stacks-1.42/htslib/cram/._cram_samtools.c
stacks-1.42/htslib/cram/cram_samtools.c
stacks-1.42/htslib/cram/._cram_samtools.h
stacks-1.42/htslib/cram/cram_samtools.h
stacks-1.42/htslib/cram/._cram_stats.c
stacks-1.42/htslib/cram/cram_stats.c
stacks-1.42/htslib/cram/._cram_stats.h
stacks-1.42/htslib/cram/cram_stats.h
stacks-1.42/htslib/cram/._cram_structs.h
stacks-1.42/htslib/cram/cram_structs.h
stacks-1.42/htslib/cram/._files.c
stacks-1.42/htslib/cram/files.c
stacks-1.42/htslib/cram/._mFILE.c
stacks-1.42/htslib/cram/mFILE.c
stacks-1.42/htslib/cram/._mFILE.h
stacks-1.42/htslib/cram/mFILE.h
stacks-1.42/htslib/cram/._misc.h
stacks-1.42/htslib/cram/misc.h
stacks-1.42/htslib/cram/._open_trace_file.c
stacks-1.42/htslib/cram/open_trace_file.c
stacks-1.42/htslib/cram/._open_trace_file.h
stacks-1.42/htslib/cram/open_trace_file.h
stacks-1.42/htslib/cram/._os.h
stacks-1.42/htslib/cram/os.h
stacks-1.42/htslib/cram/._pooled_alloc.c
stacks-1.42/htslib/cram/pooled_alloc.c
stacks-1.42/htslib/cram/._pooled_alloc.h
stacks-1.42/htslib/cram/pooled_alloc.h
stacks-1.42/htslib/cram/._rANS_byte.h
stacks-1.42/htslib/cram/rANS_byte.h
stacks-1.42/htslib/cram/._rANS_static.c
stacks-1.42/htslib/cram/rANS_static.c
stacks-1.42/htslib/cram/._rANS_static.h
stacks-1.42/htslib/cram/rANS_static.h
stacks-1.42/htslib/cram/._sam_header.c
stacks-1.42/htslib/cram/sam_header.c
stacks-1.42/htslib/cram/._sam_header.h
stacks-1.42/htslib/cram/sam_header.h
stacks-1.42/htslib/cram/._string_alloc.c
stacks-1.42/htslib/cram/string_alloc.c
stacks-1.42/htslib/cram/._string_alloc.h
stacks-1.42/htslib/cram/string_alloc.h
stacks-1.42/htslib/cram/._thread_pool.c
stacks-1.42/htslib/cram/thread_pool.c
stacks-1.42/htslib/cram/._thread_pool.h
stacks-1.42/htslib/cram/thread_pool.h
stacks-1.42/htslib/cram/._vlen.c
stacks-1.42/htslib/cram/vlen.c
stacks-1.42/htslib/cram/._vlen.h
stacks-1.42/htslib/cram/vlen.h
stacks-1.42/htslib/cram/._zfio.c
stacks-1.42/htslib/cram/zfio.c
stacks-1.42/htslib/cram/._zfio.h
stacks-1.42/htslib/cram/zfio.h
stacks-1.42/config/compile
stacks-1.42/config/depcomp
stacks-1.42/config/install-sh
stacks-1.42/config/missing
stacks-1.42/config/test-driver
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking whether g++ supports C++11 features by default... no
checking whether g++ supports C++11 features with -std=gnu++11... yes
checking for omp_set_num_threads in -lgomp... yes
checking for gzread in -lz... yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for gcc option to support OpenMP... -fopenmp
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for an ANSI C-conforming const... yes
checking for size_t... yes
checking whether closedir returns void... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for floor... no
checking for memset... yes
checking for pow... no
checking for sqrt... no
checking for gawk... (cached) gawk
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
make  all-recursive
make[1]: Entering directory `/home/iovercast/manuscript-analysis/stacks-1.42'
Making all in htslib
make[2]: Entering directory `/home/iovercast/manuscript-analysis/stacks-1.42/htslib'
echo '/* Empty config.h generated by Makefile */' > config.h
gcc -g -Wall -O2 -I.  -c -o kfunc.o kfunc.c
gcc -g -Wall -O2 -I.  -c -o knetfile.o knetfile.c
gcc -g -Wall -O2 -I.  -c -o kstring.o kstring.c
gcc -g -Wall -O2 -I.  -c -o bgzf.o bgzf.c
gcc -g -Wall -O2 -I.  -c -o faidx.o faidx.c
gcc -g -Wall -O2 -I.  -c -o hfile.o hfile.c
gcc -g -Wall -O2 -I.  -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.3.1"' > version.h
gcc -g -Wall -O2 -I.  -c -o hts.o hts.c
gcc -g -Wall -O2 -I.  -c -o md5.o md5.c
gcc -g -Wall -O2 -I.  -c -o regidx.o regidx.c
gcc -g -Wall -O2 -I.  -c -o sam.o sam.c
gcc -g -Wall -O2 -I.  -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -Wall -O2 -I.  -c -o vcf_sweep.o vcf_sweep.c
gcc -g -Wall -O2 -I.  -c -o tbx.o tbx.c
gcc -g -Wall -O2 -I.  -c -o vcf.o vcf.c
gcc -g -Wall -O2 -I.  -c -o vcfutils.o vcfutils.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_external.o cram/cram_external.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_index.o cram/cram_index.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_io.o cram/cram_io.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -Wall -O2 -I.  -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -Wall -O2 -I.  -c -o cram/files.o cram/files.c
gcc -g -Wall -O2 -I.  -c -o cram/mFILE.o cram/mFILE.c
gcc -g -Wall -O2 -I.  -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -Wall -O2 -I.  -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -Wall -O2 -I.  -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -Wall -O2 -I.  -c -o cram/sam_header.o cram/sam_header.c
gcc -g -Wall -O2 -I.  -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -Wall -O2 -I.  -c -o cram/thread_pool.o cram/thread_pool.c
gcc -g -Wall -O2 -I.  -c -o cram/vlen.o cram/vlen.c
gcc -g -Wall -O2 -I.  -c -o cram/zfio.o cram/zfio.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o faidx.o hfile.o hfile_net.o hts.o md5.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/thread_pool.o cram/vlen.o cram/zfio.o
ranlib libhts.a
make[2]: Leaving directory `/home/iovercast/manuscript-analysis/stacks-1.42/htslib'
Making all in .
make[2]: Entering directory `/home/iovercast/manuscript-analysis/stacks-1.42'
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-ustacks.o -MD -MP -MF src/.deps/ustacks-ustacks.Tpo -c -o src/ustacks-ustacks.o `test -f 'src/ustacks.cc' || echo './'`src/ustacks.cc
mv -f src/.deps/ustacks-ustacks.Tpo src/.deps/ustacks-ustacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-stacks.o -MD -MP -MF src/.deps/ustacks-stacks.Tpo -c -o src/ustacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
mv -f src/.deps/ustacks-stacks.Tpo src/.deps/ustacks-stacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-mstack.o -MD -MP -MF src/.deps/ustacks-mstack.Tpo -c -o src/ustacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc
mv -f src/.deps/ustacks-mstack.Tpo src/.deps/ustacks-mstack.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-mst.o -MD -MP -MF src/.deps/ustacks-mst.Tpo -c -o src/ustacks-mst.o `test -f 'src/mst.cc' || echo './'`src/mst.cc
mv -f src/.deps/ustacks-mst.Tpo src/.deps/ustacks-mst.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-cmb.o -MD -MP -MF src/.deps/ustacks-cmb.Tpo -c -o src/ustacks-cmb.o `test -f 'src/cmb.cc' || echo './'`src/cmb.cc
mv -f src/.deps/ustacks-cmb.Tpo src/.deps/ustacks-cmb.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-DNASeq.o -MD -MP -MF src/.deps/ustacks-DNASeq.Tpo -c -o src/ustacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
mv -f src/.deps/ustacks-DNASeq.Tpo src/.deps/ustacks-DNASeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-DNANSeq.o -MD -MP -MF src/.deps/ustacks-DNANSeq.Tpo -c -o src/ustacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
mv -f src/.deps/ustacks-DNANSeq.Tpo src/.deps/ustacks-DNANSeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-models.o -MD -MP -MF src/.deps/ustacks-models.Tpo -c -o src/ustacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc
mv -f src/.deps/ustacks-models.Tpo src/.deps/ustacks-models.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-utils.o -MD -MP -MF src/.deps/ustacks-utils.Tpo -c -o src/ustacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/ustacks-utils.Tpo src/.deps/ustacks-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-kmers.o -MD -MP -MF src/.deps/ustacks-kmers.Tpo -c -o src/ustacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
mv -f src/.deps/ustacks-kmers.Tpo src/.deps/ustacks-kmers.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-aln_utils.o -MD -MP -MF src/.deps/ustacks-aln_utils.Tpo -c -o src/ustacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
mv -f src/.deps/ustacks-aln_utils.Tpo src/.deps/ustacks-aln_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/ustacks-input.o -MD -MP -MF src/.deps/ustacks-input.Tpo -c -o src/ustacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/ustacks-input.Tpo src/.deps/ustacks-input.Po
g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o ustacks src/ustacks-ustacks.o src/ustacks-stacks.o src/ustacks-mstack.o src/ustacks-mst.o src/ustacks-cmb.o src/ustacks-DNASeq.o src/ustacks-DNANSeq.o src/ustacks-models.o src/ustacks-utils.o src/ustacks-kmers.o src/ustacks-aln_utils.o src/ustacks-input.o  -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/pstacks-pstacks.o -MD -MP -MF src/.deps/pstacks-pstacks.Tpo -c -o src/pstacks-pstacks.o `test -f 'src/pstacks.cc' || echo './'`src/pstacks.cc
mv -f src/.deps/pstacks-pstacks.Tpo src/.deps/pstacks-pstacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/pstacks-stacks.o -MD -MP -MF src/.deps/pstacks-stacks.Tpo -c -o src/pstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
mv -f src/.deps/pstacks-stacks.Tpo src/.deps/pstacks-stacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/pstacks-mstack.o -MD -MP -MF src/.deps/pstacks-mstack.Tpo -c -o src/pstacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc
mv -f src/.deps/pstacks-mstack.Tpo src/.deps/pstacks-mstack.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/pstacks-DNANSeq.o -MD -MP -MF src/.deps/pstacks-DNANSeq.Tpo -c -o src/pstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
mv -f src/.deps/pstacks-DNANSeq.Tpo src/.deps/pstacks-DNANSeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/pstacks-DNASeq.o -MD -MP -MF src/.deps/pstacks-DNASeq.Tpo -c -o src/pstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
mv -f src/.deps/pstacks-DNASeq.Tpo src/.deps/pstacks-DNASeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/pstacks-models.o -MD -MP -MF src/.deps/pstacks-models.Tpo -c -o src/pstacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc
mv -f src/.deps/pstacks-models.Tpo src/.deps/pstacks-models.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/pstacks-utils.o -MD -MP -MF src/.deps/pstacks-utils.Tpo -c -o src/pstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/pstacks-utils.Tpo src/.deps/pstacks-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/pstacks-input.o -MD -MP -MF src/.deps/pstacks-input.Tpo -c -o src/pstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/pstacks-input.Tpo src/.deps/pstacks-input.Po
g++ -fopenmp -I./htslib/htslib  -g -O2 -std=gnu++11 -fopenmp  -o pstacks src/pstacks-pstacks.o src/pstacks-stacks.o src/pstacks-mstack.o src/pstacks-DNANSeq.o src/pstacks-DNASeq.o src/pstacks-models.o src/pstacks-utils.o src/pstacks-input.o ./htslib/libhts.a -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/estacks-estacks.o -MD -MP -MF src/.deps/estacks-estacks.Tpo -c -o src/estacks-estacks.o `test -f 'src/estacks.cc' || echo './'`src/estacks.cc
mv -f src/.deps/estacks-estacks.Tpo src/.deps/estacks-estacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/estacks-stacks.o -MD -MP -MF src/.deps/estacks-stacks.Tpo -c -o src/estacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
mv -f src/.deps/estacks-stacks.Tpo src/.deps/estacks-stacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/estacks-mstack.o -MD -MP -MF src/.deps/estacks-mstack.Tpo -c -o src/estacks-mstack.o `test -f 'src/mstack.cc' || echo './'`src/mstack.cc
mv -f src/.deps/estacks-mstack.Tpo src/.deps/estacks-mstack.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/estacks-models.o -MD -MP -MF src/.deps/estacks-models.Tpo -c -o src/estacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc
mv -f src/.deps/estacks-models.Tpo src/.deps/estacks-models.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/estacks-utils.o -MD -MP -MF src/.deps/estacks-utils.Tpo -c -o src/estacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/estacks-utils.Tpo src/.deps/estacks-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/estacks-DNASeq.o -MD -MP -MF src/.deps/estacks-DNASeq.Tpo -c -o src/estacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
mv -f src/.deps/estacks-DNASeq.Tpo src/.deps/estacks-DNASeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/estacks-DNANSeq.o -MD -MP -MF src/.deps/estacks-DNANSeq.Tpo -c -o src/estacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
mv -f src/.deps/estacks-DNANSeq.Tpo src/.deps/estacks-DNANSeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/estacks-input.o -MD -MP -MF src/.deps/estacks-input.Tpo -c -o src/estacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/estacks-input.Tpo src/.deps/estacks-input.Po
g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o estacks src/estacks-estacks.o src/estacks-stacks.o src/estacks-mstack.o src/estacks-models.o src/estacks-utils.o src/estacks-DNASeq.o src/estacks-DNANSeq.o src/estacks-input.o  -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-cstacks.o -MD -MP -MF src/.deps/cstacks-cstacks.Tpo -c -o src/cstacks-cstacks.o `test -f 'src/cstacks.cc' || echo './'`src/cstacks.cc
mv -f src/.deps/cstacks-cstacks.Tpo src/.deps/cstacks-cstacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-stacks.o -MD -MP -MF src/.deps/cstacks-stacks.Tpo -c -o src/cstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
mv -f src/.deps/cstacks-stacks.Tpo src/.deps/cstacks-stacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-locus.o -MD -MP -MF src/.deps/cstacks-locus.Tpo -c -o src/cstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
mv -f src/.deps/cstacks-locus.Tpo src/.deps/cstacks-locus.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-kmers.o -MD -MP -MF src/.deps/cstacks-kmers.Tpo -c -o src/cstacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
mv -f src/.deps/cstacks-kmers.Tpo src/.deps/cstacks-kmers.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-utils.o -MD -MP -MF src/.deps/cstacks-utils.Tpo -c -o src/cstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-aln_utils.o -MD -MP -MF src/.deps/cstacks-aln_utils.Tpo -c -o src/cstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
mv -f src/.deps/cstacks-aln_utils.Tpo src/.deps/cstacks-aln_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-DNASeq.o -MD -MP -MF src/.deps/cstacks-DNASeq.Tpo -c -o src/cstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
mv -f src/.deps/cstacks-DNASeq.Tpo src/.deps/cstacks-DNASeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-DNANSeq.o -MD -MP -MF src/.deps/cstacks-DNANSeq.Tpo -c -o src/cstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
mv -f src/.deps/cstacks-DNANSeq.Tpo src/.deps/cstacks-DNANSeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-input.o -MD -MP -MF src/.deps/cstacks-input.Tpo -c -o src/cstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/cstacks-input.Tpo src/.deps/cstacks-input.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/cstacks-sql_utilities.o -MD -MP -MF src/.deps/cstacks-sql_utilities.Tpo -c -o src/cstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
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g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o cstacks src/cstacks-cstacks.o src/cstacks-stacks.o src/cstacks-locus.o src/cstacks-kmers.o src/cstacks-utils.o src/cstacks-aln_utils.o src/cstacks-DNASeq.o src/cstacks-DNANSeq.o src/cstacks-input.o src/cstacks-sql_utilities.o  -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-sstacks.o -MD -MP -MF src/.deps/sstacks-sstacks.Tpo -c -o src/sstacks-sstacks.o `test -f 'src/sstacks.cc' || echo './'`src/sstacks.cc
mv -f src/.deps/sstacks-sstacks.Tpo src/.deps/sstacks-sstacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-stacks.o -MD -MP -MF src/.deps/sstacks-stacks.Tpo -c -o src/sstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-locus.o -MD -MP -MF src/.deps/sstacks-locus.Tpo -c -o src/sstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
mv -f src/.deps/sstacks-locus.Tpo src/.deps/sstacks-locus.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-kmers.o -MD -MP -MF src/.deps/sstacks-kmers.Tpo -c -o src/sstacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
mv -f src/.deps/sstacks-kmers.Tpo src/.deps/sstacks-kmers.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-aln_utils.o -MD -MP -MF src/.deps/sstacks-aln_utils.Tpo -c -o src/sstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
mv -f src/.deps/sstacks-aln_utils.Tpo src/.deps/sstacks-aln_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-DNASeq.o -MD -MP -MF src/.deps/sstacks-DNASeq.Tpo -c -o src/sstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
mv -f src/.deps/sstacks-DNASeq.Tpo src/.deps/sstacks-DNASeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-DNANSeq.o -MD -MP -MF src/.deps/sstacks-DNANSeq.Tpo -c -o src/sstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
mv -f src/.deps/sstacks-DNANSeq.Tpo src/.deps/sstacks-DNANSeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-utils.o -MD -MP -MF src/.deps/sstacks-utils.Tpo -c -o src/sstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/sstacks-utils.Tpo src/.deps/sstacks-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-input.o -MD -MP -MF src/.deps/sstacks-input.Tpo -c -o src/sstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/sstacks-input.Tpo src/.deps/sstacks-input.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/sstacks-sql_utilities.o -MD -MP -MF src/.deps/sstacks-sql_utilities.Tpo -c -o src/sstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
mv -f src/.deps/sstacks-sql_utilities.Tpo src/.deps/sstacks-sql_utilities.Po
g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o sstacks src/sstacks-sstacks.o src/sstacks-stacks.o src/sstacks-locus.o src/sstacks-kmers.o src/sstacks-aln_utils.o src/sstacks-DNASeq.o src/sstacks-DNANSeq.o src/sstacks-utils.o src/sstacks-input.o src/sstacks-sql_utilities.o  -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-rxstacks.o -MD -MP -MF src/.deps/rxstacks-rxstacks.Tpo -c -o src/rxstacks-rxstacks.o `test -f 'src/rxstacks.cc' || echo './'`src/rxstacks.cc
mv -f src/.deps/rxstacks-rxstacks.Tpo src/.deps/rxstacks-rxstacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-stacks.o -MD -MP -MF src/.deps/rxstacks-stacks.Tpo -c -o src/rxstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
mv -f src/.deps/rxstacks-stacks.Tpo src/.deps/rxstacks-stacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-locus.o -MD -MP -MF src/.deps/rxstacks-locus.Tpo -c -o src/rxstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
mv -f src/.deps/rxstacks-locus.Tpo src/.deps/rxstacks-locus.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-DNANSeq.o -MD -MP -MF src/.deps/rxstacks-DNANSeq.Tpo -c -o src/rxstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
mv -f src/.deps/rxstacks-DNANSeq.Tpo src/.deps/rxstacks-DNANSeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-DNASeq.o -MD -MP -MF src/.deps/rxstacks-DNASeq.Tpo -c -o src/rxstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
mv -f src/.deps/rxstacks-DNASeq.Tpo src/.deps/rxstacks-DNASeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-mst.o -MD -MP -MF src/.deps/rxstacks-mst.Tpo -c -o src/rxstacks-mst.o `test -f 'src/mst.cc' || echo './'`src/mst.cc
mv -f src/.deps/rxstacks-mst.Tpo src/.deps/rxstacks-mst.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-models.o -MD -MP -MF src/.deps/rxstacks-models.Tpo -c -o src/rxstacks-models.o `test -f 'src/models.cc' || echo './'`src/models.cc
mv -f src/.deps/rxstacks-models.Tpo src/.deps/rxstacks-models.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-aln_utils.o -MD -MP -MF src/.deps/rxstacks-aln_utils.Tpo -c -o src/rxstacks-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
mv -f src/.deps/rxstacks-aln_utils.Tpo src/.deps/rxstacks-aln_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-utils.o -MD -MP -MF src/.deps/rxstacks-utils.Tpo -c -o src/rxstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/rxstacks-utils.Tpo src/.deps/rxstacks-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-input.o -MD -MP -MF src/.deps/rxstacks-input.Tpo -c -o src/rxstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/rxstacks-input.Tpo src/.deps/rxstacks-input.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-sql_utilities.o -MD -MP -MF src/.deps/rxstacks-sql_utilities.Tpo -c -o src/rxstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
mv -f src/.deps/rxstacks-sql_utilities.Tpo src/.deps/rxstacks-sql_utilities.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/rxstacks-MetaPopInfo.o -MD -MP -MF src/.deps/rxstacks-MetaPopInfo.Tpo -c -o src/rxstacks-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc
mv -f src/.deps/rxstacks-MetaPopInfo.Tpo src/.deps/rxstacks-MetaPopInfo.Po
g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o rxstacks src/rxstacks-rxstacks.o src/rxstacks-stacks.o src/rxstacks-locus.o src/rxstacks-DNANSeq.o src/rxstacks-DNASeq.o src/rxstacks-mst.o src/rxstacks-models.o src/rxstacks-aln_utils.o src/rxstacks-utils.o src/rxstacks-input.o src/rxstacks-sql_utilities.o src/rxstacks-MetaPopInfo.o  -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/hstacks-hstacks.o -MD -MP -MF src/.deps/hstacks-hstacks.Tpo -c -o src/hstacks-hstacks.o `test -f 'src/hstacks.cc' || echo './'`src/hstacks.cc
mv -f src/.deps/hstacks-hstacks.Tpo src/.deps/hstacks-hstacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/hstacks-stacks.o -MD -MP -MF src/.deps/hstacks-stacks.Tpo -c -o src/hstacks-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
mv -f src/.deps/hstacks-stacks.Tpo src/.deps/hstacks-stacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/hstacks-locus.o -MD -MP -MF src/.deps/hstacks-locus.Tpo -c -o src/hstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
mv -f src/.deps/hstacks-locus.Tpo src/.deps/hstacks-locus.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/hstacks-kmers.o -MD -MP -MF src/.deps/hstacks-kmers.Tpo -c -o src/hstacks-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
mv -f src/.deps/hstacks-kmers.Tpo src/.deps/hstacks-kmers.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/hstacks-DNASeq.o -MD -MP -MF src/.deps/hstacks-DNASeq.Tpo -c -o src/hstacks-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
mv -f src/.deps/hstacks-DNASeq.Tpo src/.deps/hstacks-DNASeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/hstacks-DNANSeq.o -MD -MP -MF src/.deps/hstacks-DNANSeq.Tpo -c -o src/hstacks-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
mv -f src/.deps/hstacks-DNANSeq.Tpo src/.deps/hstacks-DNANSeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/hstacks-utils.o -MD -MP -MF src/.deps/hstacks-utils.Tpo -c -o src/hstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/hstacks-utils.Tpo src/.deps/hstacks-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/hstacks-input.o -MD -MP -MF src/.deps/hstacks-input.Tpo -c -o src/hstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/hstacks-input.Tpo src/.deps/hstacks-input.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/hstacks-sql_utilities.o -MD -MP -MF src/.deps/hstacks-sql_utilities.Tpo -c -o src/hstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
mv -f src/.deps/hstacks-sql_utilities.Tpo src/.deps/hstacks-sql_utilities.Po
g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o hstacks src/hstacks-hstacks.o src/hstacks-stacks.o src/hstacks-locus.o src/hstacks-kmers.o src/hstacks-DNASeq.o src/hstacks-DNANSeq.o src/hstacks-utils.o src/hstacks-input.o src/hstacks-sql_utilities.o  -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_radtags-process_radtags.o -MD -MP -MF src/.deps/process_radtags-process_radtags.Tpo -c -o src/process_radtags-process_radtags.o `test -f 'src/process_radtags.cc' || echo './'`src/process_radtags.cc
mv -f src/.deps/process_radtags-process_radtags.Tpo src/.deps/process_radtags-process_radtags.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_radtags-utils.o -MD -MP -MF src/.deps/process_radtags-utils.Tpo -c -o src/process_radtags-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/process_radtags-utils.Tpo src/.deps/process_radtags-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_radtags-log_utils.o -MD -MP -MF src/.deps/process_radtags-log_utils.Tpo -c -o src/process_radtags-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
mv -f src/.deps/process_radtags-log_utils.Tpo src/.deps/process_radtags-log_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_radtags-write.o -MD -MP -MF src/.deps/process_radtags-write.Tpo -c -o src/process_radtags-write.o `test -f 'src/write.cc' || echo './'`src/write.cc
mv -f src/.deps/process_radtags-write.Tpo src/.deps/process_radtags-write.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_radtags-clean.o -MD -MP -MF src/.deps/process_radtags-clean.Tpo -c -o src/process_radtags-clean.o `test -f 'src/clean.cc' || echo './'`src/clean.cc
mv -f src/.deps/process_radtags-clean.Tpo src/.deps/process_radtags-clean.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_radtags-file_io.o -MD -MP -MF src/.deps/process_radtags-file_io.Tpo -c -o src/process_radtags-file_io.o `test -f 'src/file_io.cc' || echo './'`src/file_io.cc
mv -f src/.deps/process_radtags-file_io.Tpo src/.deps/process_radtags-file_io.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_radtags-input.o -MD -MP -MF src/.deps/process_radtags-input.Tpo -c -o src/process_radtags-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/process_radtags-input.Tpo src/.deps/process_radtags-input.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_radtags-renz.o -MD -MP -MF src/.deps/process_radtags-renz.Tpo -c -o src/process_radtags-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc
mv -f src/.deps/process_radtags-renz.Tpo src/.deps/process_radtags-renz.Po
g++ -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -fopenmp  -o process_radtags src/process_radtags-process_radtags.o src/process_radtags-utils.o src/process_radtags-log_utils.o src/process_radtags-write.o src/process_radtags-clean.o src/process_radtags-file_io.o src/process_radtags-input.o src/process_radtags-renz.o ./htslib/libhts.a -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_shortreads-process_shortreads.o -MD -MP -MF src/.deps/process_shortreads-process_shortreads.Tpo -c -o src/process_shortreads-process_shortreads.o `test -f 'src/process_shortreads.cc' || echo './'`src/process_shortreads.cc
mv -f src/.deps/process_shortreads-process_shortreads.Tpo src/.deps/process_shortreads-process_shortreads.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_shortreads-clean.o -MD -MP -MF src/.deps/process_shortreads-clean.Tpo -c -o src/process_shortreads-clean.o `test -f 'src/clean.cc' || echo './'`src/clean.cc
mv -f src/.deps/process_shortreads-clean.Tpo src/.deps/process_shortreads-clean.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_shortreads-file_io.o -MD -MP -MF src/.deps/process_shortreads-file_io.Tpo -c -o src/process_shortreads-file_io.o `test -f 'src/file_io.cc' || echo './'`src/file_io.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_shortreads-utils.o -MD -MP -MF src/.deps/process_shortreads-utils.Tpo -c -o src/process_shortreads-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_shortreads-log_utils.o -MD -MP -MF src/.deps/process_shortreads-log_utils.Tpo -c -o src/process_shortreads-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_shortreads-write.o -MD -MP -MF src/.deps/process_shortreads-write.Tpo -c -o src/process_shortreads-write.o `test -f 'src/write.cc' || echo './'`src/write.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_shortreads-kmers.o -MD -MP -MF src/.deps/process_shortreads-kmers.Tpo -c -o src/process_shortreads-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
mv -f src/.deps/process_shortreads-kmers.Tpo src/.deps/process_shortreads-kmers.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -MT src/process_shortreads-input.o -MD -MP -MF src/.deps/process_shortreads-input.Tpo -c -o src/process_shortreads-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
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g++ -fopenmp  -I./htslib/htslib  -g -O2 -std=gnu++11 -fopenmp  -o process_shortreads src/process_shortreads-process_shortreads.o src/process_shortreads-clean.o src/process_shortreads-file_io.o src/process_shortreads-utils.o src/process_shortreads-log_utils.o src/process_shortreads-write.o src/process_shortreads-kmers.o src/process_shortreads-input.o ./htslib/libhts.a -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/kmer_filter-kmer_filter.o -MD -MP -MF src/.deps/kmer_filter-kmer_filter.Tpo -c -o src/kmer_filter-kmer_filter.o `test -f 'src/kmer_filter.cc' || echo './'`src/kmer_filter.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/kmer_filter-utils.o -MD -MP -MF src/.deps/kmer_filter-utils.Tpo -c -o src/kmer_filter-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/kmer_filter-write.o -MD -MP -MF src/.deps/kmer_filter-write.Tpo -c -o src/kmer_filter-write.o `test -f 'src/write.cc' || echo './'`src/write.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/kmer_filter-kmers.o -MD -MP -MF src/.deps/kmer_filter-kmers.Tpo -c -o src/kmer_filter-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/kmer_filter-input.o -MD -MP -MF src/.deps/kmer_filter-input.Tpo -c -o src/kmer_filter-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/kmer_filter-input.Tpo src/.deps/kmer_filter-input.Po
g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o kmer_filter src/kmer_filter-kmer_filter.o src/kmer_filter-utils.o src/kmer_filter-write.o src/kmer_filter-kmers.o src/kmer_filter-input.o  -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib -g -O2 -std=gnu++11 -MT src/clone_filter-clone_filter.o -MD -MP -MF src/.deps/clone_filter-clone_filter.Tpo -c -o src/clone_filter-clone_filter.o `test -f 'src/clone_filter.cc' || echo './'`src/clone_filter.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib -g -O2 -std=gnu++11 -MT src/clone_filter-kmers.o -MD -MP -MF src/.deps/clone_filter-kmers.Tpo -c -o src/clone_filter-kmers.o `test -f 'src/kmers.cc' || echo './'`src/kmers.cc
mv -f src/.deps/clone_filter-kmers.Tpo src/.deps/clone_filter-kmers.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib -g -O2 -std=gnu++11 -MT src/clone_filter-utils.o -MD -MP -MF src/.deps/clone_filter-utils.Tpo -c -o src/clone_filter-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
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g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib -g -O2 -std=gnu++11 -MT src/clone_filter-write.o -MD -MP -MF src/.deps/clone_filter-write.Tpo -c -o src/clone_filter-write.o `test -f 'src/write.cc' || echo './'`src/write.cc
mv -f src/.deps/clone_filter-write.Tpo src/.deps/clone_filter-write.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib -g -O2 -std=gnu++11 -MT src/clone_filter-clean.o -MD -MP -MF src/.deps/clone_filter-clean.Tpo -c -o src/clone_filter-clean.o `test -f 'src/clean.cc' || echo './'`src/clean.cc
mv -f src/.deps/clone_filter-clean.Tpo src/.deps/clone_filter-clean.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib -g -O2 -std=gnu++11 -MT src/clone_filter-file_io.o -MD -MP -MF src/.deps/clone_filter-file_io.Tpo -c -o src/clone_filter-file_io.o `test -f 'src/file_io.cc' || echo './'`src/file_io.cc
mv -f src/.deps/clone_filter-file_io.Tpo src/.deps/clone_filter-file_io.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -I./htslib/htslib -g -O2 -std=gnu++11 -MT src/clone_filter-input.o -MD -MP -MF src/.deps/clone_filter-input.Tpo -c -o src/clone_filter-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/clone_filter-input.Tpo src/.deps/clone_filter-input.Po
g++ -fopenmp  -I./htslib/htslib -g -O2 -std=gnu++11 -fopenmp  -o clone_filter src/clone_filter-clone_filter.o src/clone_filter-kmers.o src/clone_filter-utils.o src/clone_filter-write.o src/clone_filter-clean.o src/clone_filter-file_io.o src/clone_filter-input.o ./htslib/libhts.a -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-genotypes.o -MD -MP -MF src/.deps/genotypes-genotypes.Tpo -c -o src/genotypes-genotypes.o `test -f 'src/genotypes.cc' || echo './'`src/genotypes.cc
mv -f src/.deps/genotypes-genotypes.Tpo src/.deps/genotypes-genotypes.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-utils.o -MD -MP -MF src/.deps/genotypes-utils.Tpo -c -o src/genotypes-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/genotypes-utils.Tpo src/.deps/genotypes-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-catalog_utils.o -MD -MP -MF src/.deps/genotypes-catalog_utils.Tpo -c -o src/genotypes-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc
mv -f src/.deps/genotypes-catalog_utils.Tpo src/.deps/genotypes-catalog_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-log_utils.o -MD -MP -MF src/.deps/genotypes-log_utils.Tpo -c -o src/genotypes-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
mv -f src/.deps/genotypes-log_utils.Tpo src/.deps/genotypes-log_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-stacks.o -MD -MP -MF src/.deps/genotypes-stacks.Tpo -c -o src/genotypes-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
mv -f src/.deps/genotypes-stacks.Tpo src/.deps/genotypes-stacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-locus.o -MD -MP -MF src/.deps/genotypes-locus.Tpo -c -o src/genotypes-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
mv -f src/.deps/genotypes-locus.Tpo src/.deps/genotypes-locus.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-DNASeq.o -MD -MP -MF src/.deps/genotypes-DNASeq.Tpo -c -o src/genotypes-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
mv -f src/.deps/genotypes-DNASeq.Tpo src/.deps/genotypes-DNASeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-DNANSeq.o -MD -MP -MF src/.deps/genotypes-DNANSeq.Tpo -c -o src/genotypes-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
mv -f src/.deps/genotypes-DNANSeq.Tpo src/.deps/genotypes-DNANSeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-aln_utils.o -MD -MP -MF src/.deps/genotypes-aln_utils.Tpo -c -o src/genotypes-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
mv -f src/.deps/genotypes-aln_utils.Tpo src/.deps/genotypes-aln_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-genotype_dictionaries.o -MD -MP -MF src/.deps/genotypes-genotype_dictionaries.Tpo -c -o src/genotypes-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo './'`src/genotype_dictionaries.cc
mv -f src/.deps/genotypes-genotype_dictionaries.Tpo src/.deps/genotypes-genotype_dictionaries.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-input.o -MD -MP -MF src/.deps/genotypes-input.Tpo -c -o src/genotypes-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/genotypes-input.Tpo src/.deps/genotypes-input.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-sql_utilities.o -MD -MP -MF src/.deps/genotypes-sql_utilities.Tpo -c -o src/genotypes-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
mv -f src/.deps/genotypes-sql_utilities.Tpo src/.deps/genotypes-sql_utilities.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-renz.o -MD -MP -MF src/.deps/genotypes-renz.Tpo -c -o src/genotypes-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc
mv -f src/.deps/genotypes-renz.Tpo src/.deps/genotypes-renz.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/genotypes-MetaPopInfo.o -MD -MP -MF src/.deps/genotypes-MetaPopInfo.Tpo -c -o src/genotypes-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc
mv -f src/.deps/genotypes-MetaPopInfo.Tpo src/.deps/genotypes-MetaPopInfo.Po
g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o genotypes src/genotypes-genotypes.o src/genotypes-utils.o src/genotypes-catalog_utils.o src/genotypes-log_utils.o src/genotypes-stacks.o src/genotypes-locus.o src/genotypes-DNASeq.o src/genotypes-DNANSeq.o src/genotypes-aln_utils.o src/genotypes-genotype_dictionaries.o src/genotypes-input.o src/genotypes-sql_utilities.o src/genotypes-renz.o src/genotypes-MetaPopInfo.o  -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-populations.o -MD -MP -MF src/.deps/populations-populations.Tpo -c -o src/populations-populations.o `test -f 'src/populations.cc' || echo './'`src/populations.cc
mv -f src/.deps/populations-populations.Tpo src/.deps/populations-populations.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-utils.o -MD -MP -MF src/.deps/populations-utils.Tpo -c -o src/populations-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/populations-utils.Tpo src/.deps/populations-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-catalog_utils.o -MD -MP -MF src/.deps/populations-catalog_utils.Tpo -c -o src/populations-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc
mv -f src/.deps/populations-catalog_utils.Tpo src/.deps/populations-catalog_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-log_utils.o -MD -MP -MF src/.deps/populations-log_utils.Tpo -c -o src/populations-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
mv -f src/.deps/populations-log_utils.Tpo src/.deps/populations-log_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-stacks.o -MD -MP -MF src/.deps/populations-stacks.Tpo -c -o src/populations-stacks.o `test -f 'src/stacks.cc' || echo './'`src/stacks.cc
mv -f src/.deps/populations-stacks.Tpo src/.deps/populations-stacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-locus.o -MD -MP -MF src/.deps/populations-locus.Tpo -c -o src/populations-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
mv -f src/.deps/populations-locus.Tpo src/.deps/populations-locus.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-DNASeq.o -MD -MP -MF src/.deps/populations-DNASeq.Tpo -c -o src/populations-DNASeq.o `test -f 'src/DNASeq.cc' || echo './'`src/DNASeq.cc
mv -f src/.deps/populations-DNASeq.Tpo src/.deps/populations-DNASeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-DNANSeq.o -MD -MP -MF src/.deps/populations-DNANSeq.Tpo -c -o src/populations-DNANSeq.o `test -f 'src/DNANSeq.cc' || echo './'`src/DNANSeq.cc
mv -f src/.deps/populations-DNANSeq.Tpo src/.deps/populations-DNANSeq.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-aln_utils.o -MD -MP -MF src/.deps/populations-aln_utils.Tpo -c -o src/populations-aln_utils.o `test -f 'src/aln_utils.cc' || echo './'`src/aln_utils.cc
mv -f src/.deps/populations-aln_utils.Tpo src/.deps/populations-aln_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-genotype_dictionaries.o -MD -MP -MF src/.deps/populations-genotype_dictionaries.Tpo -c -o src/populations-genotype_dictionaries.o `test -f 'src/genotype_dictionaries.cc' || echo './'`src/genotype_dictionaries.cc
mv -f src/.deps/populations-genotype_dictionaries.Tpo src/.deps/populations-genotype_dictionaries.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-input.o -MD -MP -MF src/.deps/populations-input.Tpo -c -o src/populations-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/populations-input.Tpo src/.deps/populations-input.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-sql_utilities.o -MD -MP -MF src/.deps/populations-sql_utilities.Tpo -c -o src/populations-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
mv -f src/.deps/populations-sql_utilities.Tpo src/.deps/populations-sql_utilities.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-renz.o -MD -MP -MF src/.deps/populations-renz.Tpo -c -o src/populations-renz.o `test -f 'src/renz.cc' || echo './'`src/renz.cc
mv -f src/.deps/populations-renz.Tpo src/.deps/populations-renz.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-export_formats.o -MD -MP -MF src/.deps/populations-export_formats.Tpo -c -o src/populations-export_formats.o `test -f 'src/export_formats.cc' || echo './'`src/export_formats.cc
mv -f src/.deps/populations-export_formats.Tpo src/.deps/populations-export_formats.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-MetaPopInfo.o -MD -MP -MF src/.deps/populations-MetaPopInfo.Tpo -c -o src/populations-MetaPopInfo.o `test -f 'src/MetaPopInfo.cc' || echo './'`src/MetaPopInfo.cc
mv -f src/.deps/populations-MetaPopInfo.Tpo src/.deps/populations-MetaPopInfo.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/populations-Vcf.o -MD -MP -MF src/.deps/populations-Vcf.Tpo -c -o src/populations-Vcf.o `test -f 'src/Vcf.cc' || echo './'`src/Vcf.cc
mv -f src/.deps/populations-Vcf.Tpo src/.deps/populations-Vcf.Po
g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o populations src/populations-populations.o src/populations-utils.o src/populations-catalog_utils.o src/populations-log_utils.o src/populations-stacks.o src/populations-locus.o src/populations-DNASeq.o src/populations-DNANSeq.o src/populations-aln_utils.o src/populations-genotype_dictionaries.o src/populations-input.o src/populations-sql_utilities.o src/populations-renz.o src/populations-export_formats.o src/populations-MetaPopInfo.o src/populations-Vcf.o  -lz -lgomp 
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/phasedstacks-phasedstacks.o -MD -MP -MF src/.deps/phasedstacks-phasedstacks.Tpo -c -o src/phasedstacks-phasedstacks.o `test -f 'src/phasedstacks.cc' || echo './'`src/phasedstacks.cc
mv -f src/.deps/phasedstacks-phasedstacks.Tpo src/.deps/phasedstacks-phasedstacks.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/phasedstacks-locus.o -MD -MP -MF src/.deps/phasedstacks-locus.Tpo -c -o src/phasedstacks-locus.o `test -f 'src/locus.cc' || echo './'`src/locus.cc
mv -f src/.deps/phasedstacks-locus.Tpo src/.deps/phasedstacks-locus.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/phasedstacks-input.o -MD -MP -MF src/.deps/phasedstacks-input.Tpo -c -o src/phasedstacks-input.o `test -f 'src/input.cc' || echo './'`src/input.cc
mv -f src/.deps/phasedstacks-input.Tpo src/.deps/phasedstacks-input.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/phasedstacks-sql_utilities.o -MD -MP -MF src/.deps/phasedstacks-sql_utilities.Tpo -c -o src/phasedstacks-sql_utilities.o `test -f 'src/sql_utilities.cc' || echo './'`src/sql_utilities.cc
mv -f src/.deps/phasedstacks-sql_utilities.Tpo src/.deps/phasedstacks-sql_utilities.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/phasedstacks-log_utils.o -MD -MP -MF src/.deps/phasedstacks-log_utils.Tpo -c -o src/phasedstacks-log_utils.o `test -f 'src/log_utils.cc' || echo './'`src/log_utils.cc
mv -f src/.deps/phasedstacks-log_utils.Tpo src/.deps/phasedstacks-log_utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/phasedstacks-utils.o -MD -MP -MF src/.deps/phasedstacks-utils.Tpo -c -o src/phasedstacks-utils.o `test -f 'src/utils.cc' || echo './'`src/utils.cc
mv -f src/.deps/phasedstacks-utils.Tpo src/.deps/phasedstacks-utils.Po
g++ -DHAVE_CONFIG_H -I.    -fopenmp  -g -O2 -std=gnu++11 -MT src/phasedstacks-catalog_utils.o -MD -MP -MF src/.deps/phasedstacks-catalog_utils.Tpo -c -o src/phasedstacks-catalog_utils.o `test -f 'src/catalog_utils.cc' || echo './'`src/catalog_utils.cc
mv -f src/.deps/phasedstacks-catalog_utils.Tpo src/.deps/phasedstacks-catalog_utils.Po
g++ -fopenmp  -g -O2 -std=gnu++11 -fopenmp  -o phasedstacks src/phasedstacks-phasedstacks.o src/phasedstacks-locus.o src/phasedstacks-input.o src/phasedstacks-sql_utilities.o src/phasedstacks-log_utils.o src/phasedstacks-utils.o src/phasedstacks-catalog_utils.o  -lz -lgomp 
make[2]: Leaving directory `/home/iovercast/manuscript-analysis/stacks-1.42'
make[1]: Leaving directory `/home/iovercast/manuscript-analysis/stacks-1.42'
Making install in htslib
make[1]: Entering directory `/home/iovercast/manuscript-analysis/stacks-1.42/htslib'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/home/iovercast/manuscript-analysis/stacks-1.42/htslib'
Making install in .
make[1]: Entering directory `/home/iovercast/manuscript-analysis/stacks-1.42'
make[2]: Entering directory `/home/iovercast/manuscript-analysis/stacks-1.42'
 /usr/bin/mkdir -p '/home/iovercast/manuscript-analysis//miniconda/bin/bin'
  /usr/bin/install -c ustacks pstacks estacks cstacks sstacks rxstacks hstacks process_radtags process_shortreads kmer_filter clone_filter genotypes populations phasedstacks '/home/iovercast/manuscript-analysis//miniconda/bin/bin'
 /usr/bin/mkdir -p '/home/iovercast/manuscript-analysis//miniconda/bin/bin'
 /usr/bin/install -c scripts/denovo_map.pl scripts/ref_map.pl scripts/export_sql.pl scripts/sort_read_pairs.pl scripts/exec_velvet.pl scripts/load_sequences.pl scripts/index_radtags.pl scripts/load_radtags.pl scripts/stacks_export_notify.pl scripts/integrate_alignments.py '/home/iovercast/manuscript-analysis//miniconda/bin/bin'
 /usr/bin/mkdir -p '/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks'
 /usr/bin/mkdir -p '/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/sql'
 /usr/bin/install -c -m 644  sql/mysql.cnf.dist sql/catalog_index.sql sql/stacks.sql sql/tag_index.sql sql/chr_index.sql '/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/sql'
 /usr/bin/mkdir -p '/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php'
 /usr/bin/install -c -m 644  php/CatalogClass.php php/annotate_marker.php php/constants.php.dist php/index.php php/tags.php php/tag.php php/Locus.php php/catalog.php php/correct_genotypes.php php/correct_genotype.php php/export_batch.php php/last_modified.php php/version.php php/catalog_genotypes.php php/db_functions.php php/header.php php/samples.php php/stacks_functions.php php/view_sequence.php php/sequence_blast.php php/pop_view.php php/sumstat_view.php php/hapstat_view.php php/fst_view.php php/phist_view.php php/stack_view.php php/population_view.js php/ajax.js php/annotate.js php/stacks.js php/export.js php/stacks.css '/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php'
 /usr/bin/mkdir -p '/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php/images'
 /usr/bin/install -c -m 644  php/images/caret-d.png php/images/caret-u.png php/images/excel_icon.png php/images/l-arrow-disabled.png php/images/l-arrow.png php/images/r-arrow-disabled.png php/images/r-arrow.png php/images/stacks_bg.png php/images/stacks_logo_rev_small.png '/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php/images'
make  install-data-hook
make[3]: Entering directory `/home/iovercast/manuscript-analysis/stacks-1.42'
sed -e 's,_VERSION_,1.42,' -e 's,_BINDIR_,/home/iovercast/manuscript-analysis//miniconda/bin/bin/,g' -e 's,_PKGDATADIR_,/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/,g' /home/iovercast/manuscript-analysis//miniconda/bin/bin/denovo_map.pl > /home/iovercast/manuscript-analysis//miniconda/bin/bin/denovo_map.pl.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/bin/denovo_map.pl.subst /home/iovercast/manuscript-analysis//miniconda/bin/bin/denovo_map.pl
chmod +x /home/iovercast/manuscript-analysis//miniconda/bin/bin/denovo_map.pl
sed -e 's,_VERSION_,1.42,' -e 's,_BINDIR_,/home/iovercast/manuscript-analysis//miniconda/bin/bin/,g' -e 's,_PKGDATADIR_,/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/,g' /home/iovercast/manuscript-analysis//miniconda/bin/bin/ref_map.pl > /home/iovercast/manuscript-analysis//miniconda/bin/bin/ref_map.pl.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/bin/ref_map.pl.subst /home/iovercast/manuscript-analysis//miniconda/bin/bin/ref_map.pl
chmod +x /home/iovercast/manuscript-analysis//miniconda/bin/bin/ref_map.pl
sed -e 's,_VERSION_,1.42,' -e 's,_PKGDATADIR_,/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/,g' /home/iovercast/manuscript-analysis//miniconda/bin/bin/export_sql.pl > /home/iovercast/manuscript-analysis//miniconda/bin/bin/export_sql.pl.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/bin/export_sql.pl.subst /home/iovercast/manuscript-analysis//miniconda/bin/bin/export_sql.pl
chmod +x /home/iovercast/manuscript-analysis//miniconda/bin/bin/export_sql.pl
sed -e 's,_VERSION_,1.42,' -e 's,_PKGDATADIR_,/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/,g' /home/iovercast/manuscript-analysis//miniconda/bin/bin/index_radtags.pl > /home/iovercast/manuscript-analysis//miniconda/bin/bin/index_radtags.pl.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/bin/index_radtags.pl.subst /home/iovercast/manuscript-analysis//miniconda/bin/bin/index_radtags.pl
chmod +x /home/iovercast/manuscript-analysis//miniconda/bin/bin/index_radtags.pl
sed -e 's,_VERSION_,1.42,' -e 's,_PKGDATADIR_,/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/,g' /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_radtags.pl > /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_radtags.pl.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_radtags.pl.subst /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_radtags.pl
chmod +x /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_radtags.pl
sed -e 's,_VERSION_,1.42,' /home/iovercast/manuscript-analysis//miniconda/bin/bin/sort_read_pairs.pl > /home/iovercast/manuscript-analysis//miniconda/bin/bin/sort_read_pairs.pl.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/bin/sort_read_pairs.pl.subst /home/iovercast/manuscript-analysis//miniconda/bin/bin/sort_read_pairs.pl
chmod +x /home/iovercast/manuscript-analysis//miniconda/bin/bin/sort_read_pairs.pl
sed -e 's,_VERSION_,1.42,' /home/iovercast/manuscript-analysis//miniconda/bin/bin/exec_velvet.pl > /home/iovercast/manuscript-analysis//miniconda/bin/bin/exec_velvet.pl.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/bin/exec_velvet.pl.subst /home/iovercast/manuscript-analysis//miniconda/bin/bin/exec_velvet.pl
chmod +x /home/iovercast/manuscript-analysis//miniconda/bin/bin/exec_velvet.pl
sed -e 's,_VERSION_,1.42,' -e 's,_PKGDATADIR_,/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/,g' /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_sequences.pl > /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_sequences.pl.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_sequences.pl.subst /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_sequences.pl
chmod +x /home/iovercast/manuscript-analysis//miniconda/bin/bin/load_sequences.pl
sed -e 's,_VERSION_,1.42,' -e 's,_PKGDATADIR_,/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/,g' -e 's,_BINDIR_,/home/iovercast/manuscript-analysis//miniconda/bin/bin/,g' \
	/home/iovercast/manuscript-analysis//miniconda/bin/bin/stacks_export_notify.pl > /home/iovercast/manuscript-analysis//miniconda/bin/bin/stacks_export_notify.pl.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/bin/stacks_export_notify.pl.subst /home/iovercast/manuscript-analysis//miniconda/bin/bin/stacks_export_notify.pl
chmod +x /home/iovercast/manuscript-analysis//miniconda/bin/bin/stacks_export_notify.pl
sed -e 's,_PKGDATADIR_,/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/,g' -e 's,_BINDIR_,/home/iovercast/manuscript-analysis//miniconda/bin/bin/,g' \
	/home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php/constants.php.dist > /home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php/constants.php.dist.subst
mv /home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php/constants.php.dist.subst /home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php/constants.php.dist
echo 1.42 > /home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php/version.php
/bin/sh /home/iovercast/manuscript-analysis/stacks-1.42/config/install-sh -d -m 755 /home/iovercast/manuscript-analysis//miniconda/bin/share/stacks/php/export
make[3]: Leaving directory `/home/iovercast/manuscript-analysis/stacks-1.42'
make[2]: Leaving directory `/home/iovercast/manuscript-analysis/stacks-1.42'
make[1]: Leaving directory `/home/iovercast/manuscript-analysis/stacks-1.42'
/home/iovercast/opt/bin/process_radtags
--2016-09-01 17:11:52--  http://catchenlab.life.illinois.edu/stacks/source/stacks-1.42.tar.gz
Resolving catchenlab.life.illinois.edu (catchenlab.life.illinois.edu)... 130.126.48.94
Connecting to catchenlab.life.illinois.edu (catchenlab.life.illinois.edu)|130.126.48.94|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 897951 (877K) [application/x-gzip]
Saving to: ‘stacks-1.42.tar.gz.1’

     0K .......... .......... .......... .......... ..........  5%  790K 1s
    50K .......... .......... .......... .......... .......... 11% 1.00M 1s
   100K .......... .......... .......... .......... .......... 17%  777K 1s
   150K .......... .......... .......... .......... .......... 22%  637K 1s
   200K .......... .......... .......... .......... .......... 28% 91.4M 1s
   250K .......... .......... .......... .......... .......... 34%  559K 1s
   300K .......... .......... .......... .......... .......... 39% 92.6M 1s
   350K .......... .......... .......... .......... .......... 45% 1.64M 0s
   400K .......... .......... .......... .......... .......... 51% 1.74M 0s
   450K .......... .......... .......... .......... .......... 57% 29.2M 0s
   500K .......... .......... .......... .......... .......... 62% 1.70M 0s
   550K .......... .......... .......... .......... .......... 68% 1.77M 0s
   600K .......... .......... .......... .......... .......... 74% 23.2M 0s
   650K .......... .......... .......... .......... .......... 79% 1.72M 0s
   700K .......... .......... .......... .......... .......... 85% 29.8M 0s
   750K .......... .......... .......... .......... .......... 91% 1.74M 0s
   800K .......... .......... .......... .......... .......... 96% 1.75M 0s
   850K .......... .......... ......                          100% 36.1M=0.5s

2016-09-01 17:11:52 (1.56 MB/s) - ‘stacks-1.42.tar.gz.1’ saved [897951/897951]

Prereqs - Download and install aftrRAD

Lots of gnarly prereqs. Also, the Genotype.pl script prompts the user a couple times to verify whether or not you want to remove individuals with lots of missing data. I modified the script for the simulated data so it just passes so I can actually automate testing.

In [338]:
%%bash -s "$WORK_DIR" -s "$AFTRRAD_DIR"
export PATH="$1/miniconda/bin:$PATH"; export "WORK_DIR=$1"; export "AFTRRAD_DIR=$2"
cd $AFTRRAD_DIR

## Get a copy of acana
wget http://www.niehs.nih.gov/research/resources/assets/docs/acana_linux_x64tgz.tgz
cp ACANA_DIR/ACANA .
cp ACANA_DIR/dnaMatrix .

## ... and mafft
wget http://mafft.cbrc.jp/alignment/software/mafft-7.305-with-extensions-src.tgz
tar -xvzf mafft-7.305-with-extensions-src.tgz
cd mafft-7.305-with-extensions/core
## This won't work on mac (`-i` flag acts different)
sed -i 's/PREFIX = \/usr\/local/PREFIX = \/$WORK_DIR\/miniconda/' Makefile
make; make install

## ... and R
## R turns out to be a complete nightmare to install if you don't have root
## using brew makes it easier, but still not v straightforward
## Brew installing R takes a while so be patient (>10 minutes)
cd $AFTRRAD_DIR
git clone https://github.com/Linuxbrew/brew.git
./brew/bin/brew install homebrew/science/r
## Copy the R binary to the miniconda bin dir so it will be available
cp brew/bin/R $WORK_DIR/miniconda/bin/

## Some hackish bullshit to get cpan working in the event you are _not_ root
## which is most everybody
wget -O- http://cpanmin.us | perl - -l ~/perl5 App::cpanminus local::lib
eval `perl -I ~/perl5/lib/perl5 -Mlocal::lib`
echo 'eval `perl -I $WORK_DIR/perl5/lib/perl5 -Mlocal::lib`' >> $WORK_DIR/.profile
echo 'export MANPATH=$WORK_DIR/perl5/man:$MANPATH' >> $WORK_DIR/.profile
source $WORK_DIR/.profile
cpanm Parallel::ForkManager

## Actually get aftrRAD
git clone https://github.com/mikesovic/AftrRAD.git
Process is interrupted.

Install dDocent

dDocent installs a bunch of business into its working directory so you have to be sure to update the PATH in a similar way to how we do it with miniconda, i.e.:

    %%bash -s "$WORK_DIR" -s "$DDOCENT_DIR"
    export PATH="$2/:$1/miniconda/bin:$PATH";

From the dDocent docs: "Now if you are using a Mac computer, things get a little trickier." This part of the manu pipeline is only tested and known to work on linux.

There is an install shell script and it tried to install lots of the deps, but several failed, which i had to install by hand (freebayes, bwa, samtools, seqtk, cd-hit-est). Drag. Freebayes turned out to be a nightmare of deps as well, so it took hours to figure out how to install. Ultimately I had to compile it on another machine and copy the binaries over. Also had to update my LD_LIBRARY_PATH to get vcflibs tools to work:

    export LD_LIBRARY_PATH=/home/iovercast/manuscript-analysis/dDocent/freebayes-src/vcflib/tabixpp/htslib/:$LD_LIBRARY_PATH
In [435]:
#%%bash -s "$WORK_DIR" -s "$DDOCENT_DIR"
#export PATH="$1/miniconda/bin:$PATH"; export "WORK_DIR=$1"; export "DDOCENT_DIR=$2"
os.chdir(WORK_DIR)
#force = True
force = ""
if force:
    shutil.rmtree(DDOCENT_DIR)
    cmd = "git clone https://github.com/jpuritz/dDocent.git"
    !$cmd

    os.chdir("dDocent")
    ## This will run for a long time and install a bunch of binaries to the dDocent dir
    cmd = "sh install_dDocent_requirements " + DDOCENT_DIR
    !$cmd
    cmd = "chmod 777 {}/dDocent".format(DDOCENT_DIR)

## test
cmd = "export PATH={}:$PATH; dDocent".format(DDOCENT_DIR)
!$cmd
/home/iovercast/manuscript-analysis/dDocent/:/home/iovercast/opt/miniconda/bin:/home/iovercast/opt/bin:/cm/shared/apps/slurm/14.11.6/sbin:/cm/shared/apps/slurm/14.11.6/bin:/cm/local/apps/gcc/5.1.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/sbin:/home/iovercast/.local/bin:/home/iovercast/bin
dDocent 2.24 

Contact [email protected] with any problems 

 
Checking for required software
The dependency freebayes is not installed or is not in your $PATH.
The dependency bwa is not installed or is not in your $PATH.
The dependency samtools is not installed or is not in your $PATH.
The dependency seqtk is not installed or is not in your $PATH.
The dependency cd-hit-est is not installed or is not in your $PATH.
/home/iovercast/manuscript-analysis/dDocent/dDocent: line 46: [: : integer expression expected
The version of Samtools installed in your $PATH is not optimized for dDocent.
Please install at least version 1.3.0


Simulation Analysis

We will use simrrls to generate some simulated RAD-seq data for testing. This is a program that was written by Deren Eaton and is available on github: github.com/dereneaton/simrrls.git. simrrls requires the python egglib module, which is somewhat painful to install. Short version:

In [ ]:
%%bash -s "$WORK_DIR"
export PATH="$1/miniconda/bin:$PATH"; export "WORK_DIR=$1"
cd $WORK_DIR

## This is the long and painful version of installing egglib.
## This is what i did, it's not super guaranteed to work on 
## different platforms, but it should be at least a guide to follow.

## no cmake on my hpc compute node, so we have to install it ourselves
## grab the silent installer and tell it to write into the 
## miniconda dir, since we're already adding that to path
wget https://cmake.org/files/v3.6/cmake-3.6.1-Linux-x86_64.sh
bash cmake-3.6.1-Linux-x86_64.sh --prefix=$WORK_DIR/miniconda --exclude-subdir
cmake --version

## Install bio++. Similar move here, we'll install to the miniconda
## directory because we don't have any assurance of root on the box
mkdir bpp
cd bpp
wget http://biopp.univ-montp2.fr/repos/sources/bpp-core-2.2.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-seq-2.2.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-popgen-2.2.0.tar.gz
tar -xvzf bpp-core-2.2.0.tar.gz
tar -xvzf bpp-seq-2.2.0.tar.gz
tar -xvzf bpp-popgen-2.2.0.tar.gz
cd bpp-core-2.2.0
cmake -DCMAKE_INSTALL_PREFIX=$WORK_DIR/miniconda
make
make install
cd ../bpp-seq-2.2.0
cmake -DCMAKE_INSTALL_PREFIX=$WORK_DIR/miniconda
make
make install
cd ../bpp-popgen-2.2.0
cmake -DCMAKE_INSTALL_PREFIX=$WORK_DIR/miniconda
make
make install

## install egglib-cpp and egglib python module
## NB: simrrls requires egglib 2 
wget http://mycor.nancy.inra.fr/egglib/releases/2.1.11/egglib-cpp-2.1.11.tar.gz
wget http://mycor.nancy.inra.fr/egglib/releases/2.1.11/egglib-py-2.1.11.tar.gz
tar -xvzf egglib-cpp-2.1.11.tar.gz
tar -xvzf egglib-py-2.1.11.tar.gz
cd egglib-cpp-2.1.11
./configure --prefix=$WORK_DIR/miniconda
make
make install
cd ../egglib-py-2.1.11/
python setup.py build --prefix=$WORK_DIR/miniconda
python setup.py install --prefix=$WORK_DIR/miniconda

## Install simrrls
git clone https://github.com/dereneaton/simrrls.git
cd simrrls
python setup.py install
simrrls --help

Simulating different RAD-datasets

Both pyRAD and stacks have undergone a lot of work since the original pyrad analysis. Because improvements have been made we want to test performance of all the current pipelines and be able to compare current to past performance. We'll follow the original pyRAD manuscript analysis (Eaton 2013) by simulating modest sized datasets with variable amounts of indels. We'll also simulate one much larger dataset. Also, because stacks has since included an option for handling gapped analysis we'll test both gapped and ungapped assembly.

Tuning simrrls indel parameter

The -I parameter for simrrls has changed since the initial pyrad manuscript, so the we had to explore new values for this parameter that will approximate the number of indels we are after. I figured out a way to run simrrls and pipe the output to muscle to get a quick idea of the indel variation for different params:

    simrrls -n 1 -L 1 -I 1 -r1 $RANDOM 2>&1 | grep 0 -A 1 | tr '@' '>' | muscle | grep T | head -n 60

If you run it like this then you can get an idea of how many indel bearing seqs are generated:

    for i in {1..50}; do simrrls -n 1 -L 1 -I .05 -r1 $RANDOM 2>&1 | grep 0 -A 1 | tr '@' '>' | muscle | grep T | head -n 40 >> rpt.txt; done
    grep "-" rpt.txt | wc -l

From experimentation:

-I value -- %loci w/ indels

  • 0.02 -- ~10%
  • 0.05 -- ~15%
  • 0.10 -- ~25%

The simulated data will live in these directories:

  • SIM_NO_DIR = WORK_DIR/simulated_data/simno
  • SIM_LO_DIR = WORK_DIR/simulated_data/simlo
  • SIM_HI_DIR = WORK_DIR/simulated_data/simhi
  • SIM_LARGE_DIR = WORK_DIR/simulated_data/simlarge

Timing:

  • 10K loci -- ~8MB -- ~ 2 minutes
  • 100K loci -- ~80MB -- ~ 20 minutes
In [326]:
import subprocess
import shutil

force = True

## Directories for the simulation data
SIM_NO_DIR=os.path.join(SIMULATION_DATA_DIR, "simno")
SIM_LO_DIR=os.path.join(SIMULATION_DATA_DIR, "simlo")
SIM_HI_DIR=os.path.join(SIMULATION_DATA_DIR, "simhi")
SIM_LARGE_DIR=os.path.join(SIMULATION_DATA_DIR, "simlarge")

for dir in [SIMULATION_DATA_DIR, SIM_NO_DIR, SIM_LO_DIR,\
            SIM_HI_DIR, SIM_LARGE_DIR]:
    if force and os.path.exists(dir):
        shutil.rmtree(dir)
    if not os.path.exists(dir):
        os.makedirs(dir)


## Tree input doesn't work right. Egglib errors.
## These are the trees from pyrad v3 manu, not sure if they ever worked there either
# newick = "(((((A:2,B:2):2,C:4):4,D:8):4,(((E:2,F:2):2,G:4):4,H:8):4):4,(((I:2,J:2):2,K:4):4,L:8):8,X:16):16;"
newick = "(((((A,B),C),D),(((E,F),G),H)),(((I,J),K),L));"
treefile = os.path.join(SIMULATION_DATA_DIR, "simtree.txt")
with open(treefile, 'w') as outfile:
    outfile.write(newick)

cmd = """\
export PATH={workdir}/miniconda/bin:$PATH; time simrrls -o {odir}/{oname} -ds 2 -L 10000 -I {indels} -r1 1
"""

## simulate no indels
call = cmd.format(workdir=WORK_DIR, odir=SIMULATION_DATA_DIR, oname="simno/simno", indels=0, tree=treefile)
print(call)
output = subprocess.check_output(call, shell=True, stderr=subprocess.STDOUT)
print(output)

## simulate low indels
call = cmd.format(workdir=WORK_DIR, odir=SIMULATION_DATA_DIR, oname="simlo/simlo", indels=0.02)
print(call)
output = subprocess.check_output(call, shell=True, stderr=subprocess.STDOUT)
print(output)

## simulate high indels
call = cmd.format(workdir=WORK_DIR, odir=SIMULATION_DATA_DIR, oname="simhi/simhi", indels=0.05)
print(call)
output = subprocess.check_output(call, shell=True, stderr=subprocess.STDOUT)
print(output)

## simulate large dataset, no indels but w/ allele dropout from mutations to cutsites
call = "export PATH={workdir}/miniconda/bin:$PATH; time simrrls -o {odir}/{oname} -ds 2 -L 100000 -mc 1 -r1 1"\
    .format(workdir=WORK_DIR, odir=SIMULATION_DATA_DIR, oname="simlarge/simlarge")
print(call)
#output = subprocess.check_output(call, shell=True, stderr=subprocess.STDOUT)
print(output)
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time simrrls -o /home/iovercast/manuscript-analysis/simulated_data/simno/simno -ds 2 -L 10000 -I 0 -r1 1


real	1m56.606s
user	1m56.326s
sys	0m0.257s

export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time simrrls -o /home/iovercast/manuscript-analysis/simulated_data/simlo/simlo -ds 2 -L 10000 -I 0.02 -r1 1


real	2m5.706s
user	2m5.544s
sys	0m0.183s

export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time simrrls -o /home/iovercast/manuscript-analysis/simulated_data/simhi/simhi -ds 2 -L 10000 -I 0.05 -r1 1


real	2m8.086s
user	2m7.912s
sys	0m0.191s

export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time simrrls -o /home/iovercast/manuscript-analysis/simulated_data/simlarge/simlarge -ds 2 -L 100000 -mc 1 -r1 1

real	2m8.086s
user	2m7.912s
sys	0m0.191s

ipyrad simulated data assembly

For simulated datasets with 10000 l00bp loci ipyrad runs in

  • v.0.3.41 ~6 minutes.
  • v.0.3.42 ~8 minutes.
  • v.0.4.0 ~4 minutes.
  • v.0.5.10 ~4 minutes.

Large dataset (100000 100bp loci)

  • v.0.4.0 ~24 minutes.
In [2]:
import ipyrad as ip
reload(ip)
ip.__version__
Out[2]:
'0.5.10'
In [3]:
import ipyrad as ip

## Set up directory structures. change the force flag if you want to
## blow everything away and restart
#force = True
force = ""
IPYRAD_SIMOUT=os.path.join(IPYRAD_DIR, "SIMDATA/")
if force and os.path.exists(IPYRAD_SIMOUT):
    shutil.rmtree(IPYRAD_SIMOUT)
if not os.path.exists(IPYRAD_SIMOUT):
    os.makedirs(IPYRAD_SIMOUT)
for outdir in ["no/", "lo/", "hi/", "large/"]:
    tmpdir = os.path.join(IPYRAD_SIMOUT, "sim"+outdir)
    if not os.path.exists(tmpdir):
        os.makedirs(tmpdir)

## go to the ipyrad simulated data output directory
#for dir in ["no", "lo", "hi", "large"]:
for dir in ["hi"]:    
    ## Set barcode and raw data files
    simout_dir = os.path.join(IPYRAD_SIMOUT, "sim"+dir)
    simdata_dir = os.path.join(SIMULATION_DATA_DIR, "sim"+dir)
    bcodes = os.path.join(simdata_dir, "sim{}_barcodes.txt".format(dir))
    fastqs = os.path.join(simdata_dir, "sim{}_R1_.fastq.gz".format(dir))
    os.chdir(simout_dir)
    ## Make a new assembly
    data = ip.Assembly("sim"+dir)
    
    ## Set padata1.set_params('project_dir', "./test_rad")
    data.set_params('raw_fastq_path', fastqs)
    data.set_params('barcodes_path', bcodes)
    data.set_params('max_low_qual_bases', 4)
    data.set_params('filter_min_trim_len', 69)
    data.set_params('max_Ns_consens', (99,99))
    data.set_params('max_Hs_consens', (99,99))
    data.set_params('max_SNPs_locus', (100, 100))
    data.set_params('min_samples_locus', 2)
    data.set_params('max_Indels_locus', (99,99))
    data.set_params('max_shared_Hs_locus', 99)
    data.set_params('trim_overhang', (2,2,2,2))

    data.write_params(force=True)

    cmd = "ipyrad -p params-sim{}.txt -s 1234567 --force".format(dir)
    print(cmd)
    !time $cmd
  New Assembly: simhi
ipyrad -p params-simhi.txt -s 1234567 --force

 -------------------------------------------------------------
  ipyrad [v.0.5.10]
  Interactive assembly and analysis of RAD-seq data
 -------------------------------------------------------------
  New Assembly: simhi
  local compute node: [40 cores] on node001

  Step 1: Demultiplexing fastq data to Samples
  [####################] 100%  chunking large files  | 0:00:00  
  [####################] 100%  sorting reads         | 0:02:11  
  [####################] 100%  writing/compressing   | 0:00:06  

  Step 2: Filtering reads 
  [####################] 100%  processing reads      | 0:00:21  

  Step 3: Clustering/Mapping reads
  [####################] 100%  dereplicating         | 0:00:00  
  [####################] 100%  clustering            | 0:00:04  
  [####################] 100%  building clusters     | 0:00:05  
  [####################] 100%  chunking              | 0:00:00  
  [####################] 100%  aligning              | 0:02:33  
  [####################] 100%  concatenating         | 0:00:02  

  Step 4: Joint estimation of error rate and heterozygosity
  [####################] 100%  inferring [H, E]      | 0:01:45  

  Step 5: Consensus base calling 
  Mean error  [0.00075 sd=0.00001]
  Mean hetero [0.00192 sd=0.00005]
  [####################] 100%  calculating depths    | 0:00:01  
  [####################] 100%  chunking clusters     | 0:00:02  
  [####################] 100%  consens calling       | 0:01:19  

  Step 6: Clustering at 0.85 similarity across 12 samples
  [####################] 100%  concat/shuffle input  | 0:00:03  
  [####################] 100%  clustering across     | 0:00:06  
  [####################] 100%  building clusters     | 0:00:04  
  [####################] 100%  aligning clusters     | 0:00:23  
  [####################] 100%  database indels       | 0:00:06  
  [####################] 100%  indexing clusters     | 0:00:08  
  [####################] 100%  building database     | 0:00:09  

  Step 7: Filter and write output files for 12 Samples
  [####################] 100%  filtering loci        | 0:00:21  
  [####################] 100%  building loci/stats   | 0:00:03  
  [####################] 100%  building vcf file     | 0:00:07  
  [####################] 100%  writing vcf file      | 0:00:00  
  [####################] 100%  building arrays       | 0:00:05  
  [####################] 100%  writing outfiles      | 0:00:03  
  Outfiles written to: ~/manuscript-analysis/ipyrad/SIMDATA/simhi/simhi_outfiles


real	11m11.744s
user	1m4.042s
sys	0m2.858s

pyrad simulated data assembly

Simulated assembly approximate runtimes:

  • 10000 l00bp loci pyrad runs in ~11 minutes.
  • 100000 100bp loci pyrad runs in ~90 minutes.

Set the default pyrad params file.

In [8]:
## Here we load the default params info into `pyrad_params`. Each simulation
## iteration will slightly modify this and write it out for their own use.

## I zipped and uuencoded the params file so it wouldn't take up so much visual room. Lol
pyrad_params = 'begin 666 <data>\nM>)R-5^]OVCH4_<Y?<:5]&&%NFA^%MFR95*W3.FFKMG;2^UBYL2%>$SNS30?3\nM^^/?=9P *Q >\'[email protected]^/CF^)QS;[-L-(*::EIQRS4(62^[email protected]*_NKJ[AF6LC\nME(0TC,))"C :90=>0&<SGEO.P%A>0Y8-PM.[CU=?KJ]^7,&!UZM7$(?PC])/\nM0LZ!"8T 2J\\._7S]&M*R# 8[6$D(7U0>@IJ!5/*$\\6I16E&7?(E5S43)#0R%\nMNV>A%))#[email protected]*4;J$>J<\\5X [!G_799#NK9<%Q0[\'_:LQ!R5554,[email protected]\nMCJDM K *<[email protected]%:Z.PM_\'7C8E)A),*@6)L<2]B./^Y /K6R0SX/!CT\\?KC[M\nM91J1)R\'<<6.UR*[email protected]))%!2/:\\C#>[email protected][]^]<E[:"Z"[email protected] 0IWMA6^CS\nM$&ZAUBKGQBB-I^.46):\\# [email protected]_TH=[$<)7(1FO;3&%2DBD!JNF<]XHFT)>\nM+HR3^[email protected]!X.S/N1+K/C[@I8(2Y?P"HRPJ*K?PA;P"[^&=Y!$S0$8SKU(\n[email protected];"B_%AV#A"&S153;OBG"-LH;DI5,F &BR;\\5Q4N,FZ8*\\+35D/,AKL\nMFEIJ5S6? OZ4S!\\-J:G0W3MC[[email protected]?>[email protected]:<YZ2,C3AJ>/ZAGS[*A\nM5>U,AI<4[2*QU%+E"_."9A1<KRIB--]7NKR_\\23C0;8,FX)J=\'+AHDHUU+^ \nMS2_&;%(E=7J3WNYNX:#[email protected]\\TGXDE2(R\\[email protected]^4+6P&\'TPE A<4Q1D\\#=T$W&J\nM=A; 7S>):>"1E^HWGI(P_JP/9>-V3.[F9 \\3XQ"W#*>[email protected]%D\\&HY%ULTC\nMC$#)<M7>4_HOSZ#D3ES9/=B3%ILR=H*^\'B(#<ZT6-<8&75(8EL)8<%\'B-]OF\nM8T*.8)^WV\'R):L;L/(+XXAC#\\%34*U3EZ;J#K"\\>.!/6G(X>[N*\'T>$"+MH"\nMRC;$&3_9;@8,\';%_<>/5GB>[;(%1F5^GF%Z5,!6U>>%EW_8*3#+&9QG$P3;P\nM3I_9!DZB%[email protected],:_FUQICI7/[email protected])T;RP>J3B)6V#L7^B;*3BL*&M2#&+_\nM_H8R6N--$T*2^:C_\'\\!))R \\4*&[email protected](_DIBTU"J,H)[email protected])M!V3&PA&%ZH^P"!\nMQ[W Z8;C6Y\\!MVVHY$H:%/POO\\WX)1_\'@,\\VP&VX^"SYLYJ\';90WS6)GDV/ \n[email protected]\\M!-(]N\'F+Q=A^[email protected]%W]]^,U,/[email protected]%F&^8UJZ;XA[MLM\n[email protected]#]CLRP1VL6LD"=-"R(TU\\H8_Z\'9(H247%X&Z[&A![OSG\\:!1%[email protected]\nM%]4C;YHB:Y\'B.$EV!.T[VC\'LSH*HTVHSCI1\\9HD6\\P(C1FZZCR!.\\,.(1($G\nMY/DP<MIYL&T&V!U0L4A+322AQ)!GLB"65.2)S,D(X;:.L;?D-%Y3_3/$D##<\nMSV740C.DO%^^J]IYQ=.SS+K/1]V2=C9\\XMA.\'"<5DJPY96T*.9U\\E&[<<3VZ\nMY\')NB]"SW>OO=,N&V*MH_H06^>-&8&F#AM7,W1J.47<5I_)-,KJ_[@;67N"U\nM#86\\YIK7FS[!W,>VV[_+,%YS50MN_&[Q4>#[email protected]]0R%PXL,16B#3VS-5PV\\6\nM$<R^U;K+#]T<U0/<>1"KXWAH%35/&ZPX>\\[email protected]_U"%[email protected]*HUL)_1>K [\nM&W;COZ/;#7[N &L\\M9_JL=UH\\[email protected]_S6:8,MS7;;IY*=Y29%4:HR8RXI+\n/NSNQ;&EX=U89_ >8=H2-\n \nend\n'
pyrad_params = pyrad_params.decode("uu").decode("zlib")
print(pyrad_params)

## If you want to make changes to the params file you can generate a new uuencoded string
## by editing the pyrad/params-pyrad.txt file and running these lines. If you run this
## at a terminal inside python shell then it'll print out nicely as one big fat line. 
#with open(os.path.join(PYRAD_DIR, "params-pyrad.txt")) as infile:
#    infile.read().encode("zlib").encode("uu")
==** parameter inputs for pyRAD version 3.0.63  **======================== affected step ==
<WORKDIR>                        ## 1. Working directory                                 (all)
<RAWFILE>              ## 2. Loc. of non-demultiplexed files (if not line 18)  (s1)
<BARCODES>              ## 3. Loc. of barcode file (if not line 18)             (s1)
vsearch                   ## 4. command (or path) to call vsearch (or usearch)    (s3,s6)
muscle                    ## 5. command (or path) to call muscle                  (s3,s7)
TGCAG                     ## 6. Restriction overhang (e.g., C|TGCAG -> TGCAG)     (s1,s2)
13                         ## 7. N processors (parallel)                           (all)
6                         ## 8. Mindepth: min coverage for a cluster              (s4,s5)
4                         ## 9. NQual: max # sites with qual < 20 (or see line 20)(s2)
.85                       ## 10. Wclust: clustering threshold as a decimal        (s3,s6)
rad                       ## 11. Datatype: rad,gbs,pairgbs,pairddrad,(others:see docs)(all)
2                         ## 12. MinCov: min samples in a final locus             (s7)
99                         ## 13. MaxSH: max inds with shared hetero site          (s7)
c85d6m2p3H3N3                 ## 14. Prefix name for final output (no spaces)         (s7)
==== optional params below this line ===================================  affected step ==
                       ## 15.opt.: select subset (prefix* only selector)            (s2-s7)
                       ## 16.opt.: add-on (outgroup) taxa (list or prefix*)         (s6,s7)
                       ## 17.opt.: exclude taxa (list or prefix*)                   (s7)
                      ## 18.opt.: loc. of de-multiplexed data                      (s2)
0                       ## 19.opt.: maxM: N mismatches in barcodes (def= 1)          (s1)
                       ## 20.opt.: phred Qscore offset (def= 33)                    (s2)
                       ## 21.opt.: filter: def=0=NQual 1=NQual+adapters. 2=strict   (s2)
                       ## 22.opt.: a priori E,H (def= 0.001,0.01, if not estimated) (s5)
99                       ## 23.opt.: maxN: max Ns in a cons seq (def=5)               (s5)
99                       ## 24.opt.: maxH: max heterozyg. sites in cons seq (def=5)   (s5)
                       ## 25.opt.: ploidy: max alleles in cons seq (def=2;see docs) (s4,s5)
                       ## 26.opt.: maxSNPs: (def=100). Paired (def=100,100)         (s7)
99                       ## 27.opt.: maxIndels: within-clust,across-clust (def. 3,99) (s3,s7)
                       ## 28.opt.: random number seed (def. 112233)              (s3,s6,s7)
                       ## 29.opt.: trim overhang left,right on final loci, def(0,0) (s7)
                       ## 30.opt.: output formats: p,n,a,s,v,u,t,m,k,g,* (see docs) (s7)
                       ## 31.opt.: maj. base call at depth>x<mindepth (def.x=mindepth) (s5)
                       ## 32.opt.: keep trimmed reads (def=0). Enter min length.    (s2)
                       ## 33.opt.: max stack size (int), def= max(500,mean+2*SD)    (s3)
                       ## 34.opt.: minDerep: exclude dereps with <= N copies, def=1 (s3)
                       ## 35.opt.: use hierarchical clustering (def.=0, 1=yes)      (s6)
                       ## 36.opt.: repeat masking (def.=1='dust' method, 0=no)      (s3,s6)
                       ## 37.opt.: vsearch max threads per job (def.=6; see docs)   (s3,s6)
==== optional: list group/clade assignments below this line (see docs) ==================

In [9]:
import subprocess

## Set up directory structures. change the force flag if you want to
## blow everything away and restart
# force = True
force = ""
PYRAD_SIMOUT=os.path.join(PYRAD_DIR, "SIMDATA/")
if force and os.path.exists(PYRAD_SIMOUT):
    shutil.rmtree(PYRAD_SIMOUT)
if not os.path.exists(PYRAD_SIMOUT):
    os.makedirs(PYRAD_SIMOUT)
for outdir in ["no/", "lo/", "hi/", "large/"]:
    tmpdir = os.path.join(PYRAD_SIMOUT, "sim"+outdir)
    if not os.path.exists(tmpdir):
        os.makedirs(tmpdir)

## go to the pyrad simulated data output directory
for dir in ["no", "lo", "hi", "large"]:
    ## Set barcode and raw data files
    simdata_dir = os.path.join(SIMULATION_DATA_DIR, "sim"+dir)
    bcodes = os.path.join(simdata_dir, "sim{}_barcodes.txt".format(dir))
    fastqs = os.path.join(simdata_dir, "sim{}_R1_.fastq.gz".format(dir))
    
    ## Set output directory and params file
    simout_dir = os.path.join(PYRAD_SIMOUT, "sim"+dir)
    my_params_file = os.path.join(simout_dir, "params{}-pyrad.txt".format(dir))
    
    ## Grab the generic pyrad params file and modify it for this run
    my_params = pyrad_params.replace("<WORKDIR>", simout_dir)
    my_params = my_params.replace("<RAWFILE>", fastqs)
    my_params = my_params.replace("<BARCODES>", bcodes)

    ## Write the params out to a file
    with open(my_params_file, 'w') as outfile:
        outfile.write(my_params)

    cmd = "export PATH={workdir}/miniconda/bin:$PATH; ".format(workdir=WORK_DIR)
    cmd += "time pyrad -p {params_file} -s 1234567".format(params_file=my_params_file)

    ## Good sub for testing
    #cmd += "time pyrad --version"

    print(cmd)
    output = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT)
    print(output)
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time pyrad -p /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simno/paramsno-pyrad.txt -s 1234567


     ------------------------------------------------------------
      pyRAD : RADseq for phylogenetics & introgression analyses
     ------------------------------------------------------------


	step 1: sorting reads by barcode
	 .	step 2: editing raw reads 
	............
	de-replicating files for clustering...

	step 3: within-sample clustering of 12 samples at 
	        '.85' similarity. Running 12 parallel jobs
	 	with up to 6 threads per job. If needed, 
		adjust to avoid CPU and MEM limits

	sample 1D_0 finished, 10000 loci
	sample 3I_0 finished, 10000 loci
	sample 3J_0 finished, 10000 loci
	sample 3K_0 finished, 10000 loci
	sample 1A_0 finished, 10000 loci
	sample 2F_0 finished, 10000 loci
	sample 1B_0 finished, 10000 loci
	sample 2E_0 finished, 10000 loci
	sample 2H_0 finished, 10000 loci
	sample 1C_0 finished, 10000 loci
	sample 3L_0 finished, 10000 loci
	sample 2G_0 finished, 10000 loci

	step 4: estimating error rate and heterozygosity
	............
	step 5: creating consensus seqs for 12 samples, using H=0.00198 E=0.00075
	............
	step 6: clustering across 12 samples at '.85' similarity 

vsearch v2.0.3_linux_x86_64, 125.9GB RAM, 40 cores
https://github.com/torognes/vsearch

Reading file /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simno/clust.85/cat.haplos_ 100%
10919996 nt in 120000 seqs, min 90, max 91, avg 91
Counting unique k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 10000 Size min 12, max 12, avg 12.0
Singletons: 0, 0.0% of seqs, 0.0% of clusters

	finished clustering
	ingroup 1A_0,1B_0,1C_0,1D_0,2E_0,2F_0,2G_0,2H_0,3I_0,3J_0,3K_0,3L_0
	addon 
	exclude 
	.............
	final stats written to:
	 /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simno/stats/c85d6m2p3H3N3.stats
	output files being written to:
	 /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simno/outfiles/ directory


real	11m6.442s
user	105m7.340s
sys	12m15.424s

export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time pyrad -p /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simlo/paramslo-pyrad.txt -s 1234567


     ------------------------------------------------------------
      pyRAD : RADseq for phylogenetics & introgression analyses
     ------------------------------------------------------------


	step 1: sorting reads by barcode
	 .	step 2: editing raw reads 
	............
	de-replicating files for clustering...

	step 3: within-sample clustering of 12 samples at 
	        '.85' similarity. Running 12 parallel jobs
	 	with up to 6 threads per job. If needed, 
		adjust to avoid CPU and MEM limits

	sample 1D_0 finished, 10000 loci
	sample 2E_0 finished, 10000 loci
	sample 2H_0 finished, 10000 loci
	sample 1A_0 finished, 10000 loci
	sample 1C_0 finished, 10000 loci
	sample 1B_0 finished, 10000 loci
	sample 3L_0 finished, 10000 loci
	sample 2G_0 finished, 10000 loci
	sample 2F_0 finished, 10000 loci
	sample 3K_0 finished, 10000 loci
	sample 3J_0 finished, 10000 loci
	sample 3I_0 finished, 10000 loci

	step 4: estimating error rate and heterozygosity
	............
	step 5: creating consensus seqs for 12 samples, using H=0.00195 E=0.00075
	............
	step 6: clustering across 12 samples at '.85' similarity 

vsearch v2.0.3_linux_x86_64, 125.9GB RAM, 40 cores
https://github.com/torognes/vsearch

Reading file /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simlo/clust.85/cat.haplos_ 100%
10920527 nt in 120000 seqs, min 90, max 94, avg 91
Counting unique k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 10000 Size min 12, max 12, avg 12.0
Singletons: 0, 0.0% of seqs, 0.0% of clusters

	finished clustering
	ingroup 1A_0,1B_0,1C_0,1D_0,2E_0,2F_0,2G_0,2H_0,3I_0,3J_0,3K_0,3L_0
	addon 
	exclude 
	.............
	final stats written to:
	 /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simlo/stats/c85d6m2p3H3N3.stats
	output files being written to:
	 /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simlo/outfiles/ directory


real	11m2.628s
user	104m0.546s
sys	12m28.283s

export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time pyrad -p /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simhi/paramshi-pyrad.txt -s 1234567


     ------------------------------------------------------------
      pyRAD : RADseq for phylogenetics & introgression analyses
     ------------------------------------------------------------


	step 1: sorting reads by barcode
	 .	step 2: editing raw reads 
	............
	de-replicating files for clustering...

	step 3: within-sample clustering of 12 samples at 
	        '.85' similarity. Running 12 parallel jobs
	 	with up to 6 threads per job. If needed, 
		adjust to avoid CPU and MEM limits

	sample 3I_0 finished, 10000 loci
	sample 1D_0 finished, 10000 loci
	sample 2H_0 finished, 10000 loci
	sample 2G_0 finished, 10000 loci
	sample 1A_0 finished, 10000 loci
	sample 2E_0 finished, 10000 loci
	sample 1B_0 finished, 10000 loci
	sample 3K_0 finished, 10000 loci
	sample 3J_0 finished, 10000 loci
	sample 2F_0 finished, 10001 loci
	sample 3L_0 finished, 10000 loci
	sample 1C_0 finished, 10000 loci

	step 4: estimating error rate and heterozygosity
	............
	step 5: creating consensus seqs for 12 samples, using H=0.00191 E=0.00075
	............
	step 6: clustering across 12 samples at '.85' similarity 

vsearch v2.0.3_linux_x86_64, 125.9GB RAM, 40 cores
https://github.com/torognes/vsearch

Reading file /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simhi/clust.85/cat.haplos_ 100%
10921211 nt in 120000 seqs, min 90, max 94, avg 91
Counting unique k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 10002 Size min 1, max 12, avg 12.0
Singletons: 1, 0.0% of seqs, 0.0% of clusters

	finished clustering
	ingroup 1A_0,1B_0,1C_0,1D_0,2E_0,2F_0,2G_0,2H_0,3I_0,3J_0,3K_0,3L_0
	addon 
	exclude 
	.............
	final stats written to:
	 /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simhi/stats/c85d6m2p3H3N3.stats
	output files being written to:
	 /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simhi/outfiles/ directory


real	11m5.615s
user	103m53.529s
sys	12m30.926s

export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time pyrad -p /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simlarge/paramslarge-pyrad.txt -s 1234567


     ------------------------------------------------------------
      pyRAD : RADseq for phylogenetics & introgression analyses
     ------------------------------------------------------------


	step 1: sorting reads by barcode
	 .	step 2: editing raw reads 
	............
	de-replicating files for clustering...

	step 3: within-sample clustering of 12 samples at 
	        '.85' similarity. Running 12 parallel jobs
	 	with up to 6 threads per job. If needed, 
		adjust to avoid CPU and MEM limits

	sample 2G_0 finished, 96973 loci
	sample 3J_0 finished, 96941 loci
	sample 3I_0 finished, 96934 loci
	sample 3K_0 finished, 96942 loci
	sample 2H_0 finished, 96978 loci
	sample 1D_0 finished, 97002 loci
	sample 1C_0 finished, 96950 loci
	sample 1A_0 finished, 96943 loci
	sample 2E_0 finished, 96985 loci
	sample 2F_0 finished, 96943 loci
	sample 3L_0 finished, 96964 loci
	sample 1B_0 finished, 96980 loci

	step 4: estimating error rate and heterozygosity
	............
	step 5: creating consensus seqs for 12 samples, using H=0.00197 E=0.00075
	............
	step 6: clustering across 12 samples at '.85' similarity 

vsearch v2.0.3_linux_x86_64, 125.9GB RAM, 40 cores
https://github.com/torognes/vsearch

Reading file /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simlarge/clust.85/cat.haplos_ 100%
105866781 nt in 1163372 seqs, min 90, max 91, avg 91
Counting unique k-mers 100%
Clustering 100%
Sorting clusters 100%
Writing clusters 100%
Clusters: 99999 Size min 1, max 12, avg 11.6
Singletons: 48, 0.0% of seqs, 0.0% of clusters

	finished clustering
	ingroup 1A_0,1B_0,1C_0,1D_0,2E_0,2F_0,2G_0,2H_0,3I_0,3J_0,3K_0,3L_0
	addon 
	exclude 
	.............
	final stats written to:
	 /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simlarge/stats/c85d6m2p3H3N3.stats
	output files being written to:
	 /home/iovercast/manuscript-analysis/pyrad/SIMDATA/simlarge/outfiles/ directory


real	92m41.293s
user	815m59.288s
sys	164m25.130s

stacks simulated data assembly

Output for stacks will be a bit trickier bcz we'll run gapped, ungapped and default on all sim data

WORK_DIR
    |____stacks
            |___SIMOUT
                    |___gapped
                           |____simno
                           |____simlo
                           |____simhi
                    |____ungapped
                    |
                    |____default

We'll make calls to stacks that will look kind of like this: ```

  • process_radtags args
    • -f input file
    • -i gzfastq
    • -b barcodes file
    • -e pstI
    • -o output dir

process_radtags -f simnoR1.fastq.gz -i gzfastq -b simno_barcodes.txt -e pstI -o simout

  • denovo_map.pl args

    • -m 2: Minimum depth to make a stack
    • -M 10: Number of mismatches per locus within individuals
    • -N 10: Number of allowed mismatches in secondary reads
    • -n 10: Number of mismatches when clustering across individuals

    Housekeeping flags:

    • -T 40: Number of threads
    • -b 1: Batch id (Can be anything)
    • -S: Disable sql

denovo_map.pl -m 2 -M 10 -N 10 -n 10 -T 40 -b 1 -S --gapped -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -X 'populations:-m 6' -X 'ustacks:--max_locus_stacks 2' -o /home/iovercast/manuscript-analysis/stacks/REALDATA/gapped/ -s

Times:

  • Demux small - 15 seconds
  • Demux large - 2m30s
  • denovo_map small -
  • denovo_map large - 23m
In [335]:
## These are the python variables for the main stacks simout paths: 
## STACKS_GAP_SIMOUT, STACKS_UNGAP_SIMOUT, STACKS_DEFAULT_SIMOUT

STACKS_SIMOUT=os.path.join(STACKS_DIR, "SIMDATA/")
STACKS_GAP_SIMOUT=os.path.join(STACKS_SIMOUT, "gapped/")
STACKS_UNGAP_SIMOUT=os.path.join(STACKS_SIMOUT, "ungapped/")
STACKS_DEFAULT_SIMOUT=os.path.join(STACKS_SIMOUT, "default/")

force = True
#force = ""
if force and os.path.exists(STACKS_SIMOUT):
    shutil.rmtree(STACKS_SIMOUT)
if not os.path.exists(STACKS_SIMOUT):
    os.makedirs(STACKS_SIMOUT)

## Make the sumulation output directories if they don't already exist
for dir in [STACKS_GAP_SIMOUT, STACKS_UNGAP_SIMOUT, STACKS_DEFAULT_SIMOUT]:
    if not os.path.exists(dir):
        os.makedirs(dir)
    for outdir in ["no/", "lo/", "hi/", "large/"]:
        tmpdir = os.path.join(dir, "sim"+outdir)
        if not os.path.exists(tmpdir):
            os.makedirs(tmpdir)

## Do the stacks sim analysis
for dir in [STACKS_GAP_SIMOUT, STACKS_UNGAP_SIMOUT, STACKS_DEFAULT_SIMOUT]:

    for sim in ["no", "lo", "hi", "large"]:
        print("##################################")
        print("Doing - " + dir + " - sim" + sim)
        print("##################################")
        ## Where simulation results will be written
        simout_dir = os.path.join(dir, "sim"+sim)
        
        ## Where the rawdata and barcodes live
        simdata_dir = os.path.join(SIMULATION_DATA_DIR, "sim"+sim)
        ## We can just use the sim barcodes file as the stacks population map
        ## because all it really is doing is reading the first column, which
        ## is the names of samples to use in denovo_map.pl
        ipyrad_bcodes = os.path.join(simdata_dir, "sim{}_barcodes.txt".format(sim))
        fastqs = os.path.join(simdata_dir, "sim{}_R1_.fastq.gz".format(sim))

        ## Munge the ipyrad barcodes file into the format stacks wants for the population map
        ## file (ie sample name then population). Here we just assign all samples to be from 
        ## population 1
        popmap = os.path.join(simout_dir, "stacks_popmap.txt")
        with open(ipyrad_bcodes) as infile:
            with open(popmap, 'w') as outfile:
                lines = infile.readlines()
                for line in lines:
                    ## This is just setting all samples to population 1 
                    outfile.write(line.split()[0]+"\t1\n")
        
        ## Munge the sim barcodes file into the format that stacks wants
        ## basically the inverse of what ipyrad uses barcode first then sample name
        ## There is probably a fancier/smarter way to do this, but this works.
        bcodes = os.path.join(simout_dir, "stacks_barcodes.txt")
        with open(ipyrad_bcodes, 'r') as infile:
            with open(bcodes, 'w') as outfile:
                lines = infile.readlines()
                for line in lines:
                    if line:
                        outfile.write("\t".join(line.split()[::-1])+"\n")

        ## Export the path so we can actually find the binaries
        cmd = "export PATH={workdir}/miniconda/bin:$PATH; ".format(workdir=WORK_DIR)

        ## Add the command to process_radtags.
        ## Yes we don't have to do this over and over, but it's fast, and also ipyrad/pyrad
        ## are paying the same demultiplex penalty for every run.
        cmd += "time process_radtags -f {simdata} -i gzfastq -b {barcodes} -e pstI -o {simout}; "\
            .format(simdata=fastqs, barcodes=bcodes, simout=simout_dir)
   
        ## Toggle the dryrun flag for testing
        #DRYRUN="-d"
        DRYRUN=""

        ## Don't add all the fancy stuff if you just want to do the default assembly
        ADDITIONAL_PARAMS = ""
        GAPPED = ""
        if not dir == STACKS_DEFAULT_SIMOUT:
            ADDITIONAL_PARAMS = " -m 2 -M 10 -N 10 -n 10 "
        if dir == STACKS_GAP_SIMOUT:
            ADDITIONAL_PARAMS += " --gapped "
            
        OUTPUT_FORMATS = "--vcf --genepop --structure --phase --fastphase --phylip "
        cmd += "time denovo_map.pl -T 40 -b 1 -S " + DRYRUN + ADDITIONAL_PARAMS\
        + " -X \'populations:" + OUTPUT_FORMATS + "\'"\
        + " -o " + simout_dir + " --samples " + simout_dir + " -O " + popmap 

        print(cmd)
        output = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT)
        print(output)
##################################
Doing - /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/ - simno
##################################
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time process_radtags -f /home/iovercast/manuscript-analysis/simulated_data/simno/simno_R1_.fastq.gz -i gzfastq -b /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/stacks_barcodes.txt -e pstI -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno; time denovo_map.pl -T 40 -b 1 -S  -m 2 -M 10 -N 10 -n 10  --gapped  -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno --samples /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -O /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/stacks_popmap.txt
Processing single-end data.
Using Phred+33 encoding for quality scores.
Found 1 input file(s).
Searching for single-end, inlined barcodes.
Loaded 12 barcodes (9bp).
Processing file 1 of 1 [simno_R1_.fastq.gz]
  2398782 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 2398782 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/process_radtags.log'

2398782 total sequences;
  0 ambiguous barcode drops;
  0 low quality read drops;
  0 ambiguous RAD-Tag drops;
2398782 retained reads.

real	0m14.880s
user	0m14.727s
sys	0m0.024s
Parsed population map: 12 files in 1 population and 1 group.
Found 12 sample file(s).
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1A_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 1 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   1 of  12 [1A_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1B_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 2 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   2 of  12 [1B_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1C_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 3 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   3 of  12 [1C_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1D_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 4 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   4 of  12 [1D_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2E_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 5 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   5 of  12 [2E_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2F_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 6 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   6 of  12 [2F_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2G_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 7 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   7 of  12 [2G_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2H_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 8 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   8 of  12 [2H_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3I_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 9 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   9 of  12 [3I_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3J_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 10 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file  10 of  12 [3J_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3K_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 11 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file  11 of  12 [3K_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3L_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -i 12 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file  12 of  12 [3L_0]

Depths of Coverage for Processed Samples:
1A_0: 19.953x
1B_0: 19.9645x
1C_0: 19.9678x
1D_0: 20.018x
2E_0: 19.9596x
2F_0: 19.9424x
2G_0: 20.0055x
2H_0: 19.989x
3I_0: 19.9392x
3J_0: 19.9353x
3K_0: 19.9284x
3L_0: 19.9928x

Generating catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/cstacks -b 1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3L_0  -p 40 -n 10 --gapped  2>&1
Matching samples to the catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/sstacks -b 1 -c /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/batch_1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/3L_0  -p 40 --gapped  2>&1
Calculating population-level summary statistics
/home/iovercast/manuscript-analysis/miniconda/bin/populations -b 1 -P /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno -s -t 40 --vcf --genepop --structure --phase --fastphase --phylip  -M /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simno/stacks_popmap.txt 2>&1

real	2m13.996s
user	12m57.180s
sys	0m5.520s

##################################
Doing - /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/ - simlo
##################################
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time process_radtags -f /home/iovercast/manuscript-analysis/simulated_data/simlo/simlo_R1_.fastq.gz -i gzfastq -b /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/stacks_barcodes.txt -e pstI -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo; time denovo_map.pl -T 40 -b 1 -S  -m 2 -M 10 -N 10 -n 10  --gapped  -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo --samples /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -O /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/stacks_popmap.txt
Processing single-end data.
Using Phred+33 encoding for quality scores.
Found 1 input file(s).
Searching for single-end, inlined barcodes.
Loaded 12 barcodes (9bp).
Processing file 1 of 1 [simlo_R1_.fastq.gz]
  2397592 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 2397592 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/process_radtags.log'

2397592 total sequences;
  0 ambiguous barcode drops;
  0 low quality read drops;
  0 ambiguous RAD-Tag drops;
2397592 retained reads.

real	0m14.630s
user	0m14.476s
sys	0m0.023s
Parsed population map: 12 files in 1 population and 1 group.
Found 12 sample file(s).
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1A_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 1 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   1 of  12 [1A_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1B_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 2 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   2 of  12 [1B_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1C_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 3 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   3 of  12 [1C_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1D_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 4 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   4 of  12 [1D_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2E_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 5 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   5 of  12 [2E_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2F_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 6 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   6 of  12 [2F_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2G_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 7 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   7 of  12 [2G_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2H_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 8 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   8 of  12 [2H_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3I_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 9 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   9 of  12 [3I_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3J_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 10 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file  10 of  12 [3J_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3K_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 11 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file  11 of  12 [3K_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3L_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -i 12 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file  12 of  12 [3L_0]

Depths of Coverage for Processed Samples:
1A_0: 19.9639x
1B_0: 19.9531x
1C_0: 19.9836x
1D_0: 19.9599x
2E_0: 19.9959x
2F_0: 19.9282x
2G_0: 19.9601x
2H_0: 19.9246x
3I_0: 19.9341x
3J_0: 19.9345x
3K_0: 19.9455x
3L_0: 19.9836x

Generating catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/cstacks -b 1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3L_0  -p 40 -n 10 --gapped  2>&1
Matching samples to the catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/sstacks -b 1 -c /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/batch_1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/3L_0  -p 40 --gapped  2>&1
Calculating population-level summary statistics
/home/iovercast/manuscript-analysis/miniconda/bin/populations -b 1 -P /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo -s -t 40 --vcf --genepop --structure --phase --fastphase --phylip  -M /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simlo/stacks_popmap.txt 2>&1

real	1m23.827s
user	10m11.612s
sys	0m4.204s

##################################
Doing - /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/ - simhi
##################################
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time process_radtags -f /home/iovercast/manuscript-analysis/simulated_data/simhi/simhi_R1_.fastq.gz -i gzfastq -b /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/stacks_barcodes.txt -e pstI -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi; time denovo_map.pl -T 40 -b 1 -S  -m 2 -M 10 -N 10 -n 10  --gapped  -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi --samples /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -O /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/stacks_popmap.txt
Processing single-end data.
Using Phred+33 encoding for quality scores.
Found 1 input file(s).
Searching for single-end, inlined barcodes.
Loaded 12 barcodes (9bp).
Processing file 1 of 1 [simhi_R1_.fastq.gz]
  2400054 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 2400054 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/process_radtags.log'

2400054 total sequences;
  0 ambiguous barcode drops;
  0 low quality read drops;
  0 ambiguous RAD-Tag drops;
2400054 retained reads.

real	0m14.621s
user	0m14.574s
sys	0m0.025s
Parsed population map: 12 files in 1 population and 1 group.
Found 12 sample file(s).
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1A_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 1 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   1 of  12 [1A_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1B_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 2 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   2 of  12 [1B_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1C_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 3 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   3 of  12 [1C_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1D_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 4 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   4 of  12 [1D_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2E_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 5 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   5 of  12 [2E_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2F_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 6 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   6 of  12 [2F_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2G_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 7 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   7 of  12 [2G_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2H_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 8 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   8 of  12 [2H_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3I_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 9 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file   9 of  12 [3I_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3J_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 10 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file  10 of  12 [3J_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3K_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 11 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file  11 of  12 [3K_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3L_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -i 12 -r -m 2 -p 40 -M 10 -N 10 --gapped  2>&1
Identifying unique stacks; file  12 of  12 [3L_0]

Depths of Coverage for Processed Samples:
1A_0: 19.9321x
1B_0: 19.9699x
1C_0: 19.9865x
1D_0: 20.0289x
2E_0: 19.9526x
2F_0: 19.9634x
2G_0: 19.9455x
2H_0: 19.9461x
3I_0: 19.9013x
3J_0: 19.9012x
3K_0: 19.938x
3L_0: 19.9768x

Generating catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/cstacks -b 1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3L_0  -p 40 -n 10 --gapped  2>&1
Matching samples to the catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/sstacks -b 1 -c /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/batch_1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/3L_0  -p 40 --gapped  2>&1
Calculating population-level summary statistics
/home/iovercast/manuscript-analysis/miniconda/bin/populations -b 1 -P /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi -s -t 40 --vcf --genepop --structure --phase --fastphase --phylip  -M /home/iovercast/manuscript-analysis/stacks/SIMDATA/gapped/simhi/stacks_popmap.txt 2>&1

real	1m53.167s
user	12m41.126s
sys	0m4.751s

##################################
Doing - /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/ - simno
##################################
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time process_radtags -f /home/iovercast/manuscript-analysis/simulated_data/simno/simno_R1_.fastq.gz -i gzfastq -b /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/stacks_barcodes.txt -e pstI -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno; time denovo_map.pl -T 40 -b 1 -S  -m 2 -M 10 -N 10 -n 10  -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno --samples /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -O /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/stacks_popmap.txt
Processing single-end data.
Using Phred+33 encoding for quality scores.
Found 1 input file(s).
Searching for single-end, inlined barcodes.
Loaded 12 barcodes (9bp).
Processing file 1 of 1 [simno_R1_.fastq.gz]
  2398782 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 2398782 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/process_radtags.log'

2398782 total sequences;
  0 ambiguous barcode drops;
  0 low quality read drops;
  0 ambiguous RAD-Tag drops;
2398782 retained reads.

real	0m14.541s
user	0m14.493s
sys	0m0.014s
Parsed population map: 12 files in 1 population and 1 group.
Found 12 sample file(s).
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1A_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 1 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   1 of  12 [1A_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1B_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 2 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   2 of  12 [1B_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1C_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 3 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   3 of  12 [1C_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1D_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 4 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   4 of  12 [1D_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2E_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 5 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   5 of  12 [2E_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2F_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 6 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   6 of  12 [2F_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2G_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 7 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   7 of  12 [2G_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2H_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 8 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   8 of  12 [2H_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3I_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 9 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   9 of  12 [3I_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3J_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 10 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file  10 of  12 [3J_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3K_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 11 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file  11 of  12 [3K_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3L_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -i 12 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file  12 of  12 [3L_0]

Depths of Coverage for Processed Samples:
1A_0: 19.953x
1B_0: 19.9645x
1C_0: 19.9678x
1D_0: 20.018x
2E_0: 19.9596x
2F_0: 19.9424x
2G_0: 20.0055x
2H_0: 19.989x
3I_0: 19.9392x
3J_0: 19.9353x
3K_0: 19.9284x
3L_0: 19.9928x

Generating catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/cstacks -b 1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3L_0  -p 40 -n 10 2>&1
Matching samples to the catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/sstacks -b 1 -c /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/batch_1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/3L_0  -p 40 2>&1
Calculating population-level summary statistics
/home/iovercast/manuscript-analysis/miniconda/bin/populations -b 1 -P /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno -s -t 40 --vcf --genepop --structure --phase --fastphase --phylip  -M /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simno/stacks_popmap.txt 2>&1

real	1m47.509s
user	12m10.832s
sys	0m4.458s

##################################
Doing - /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/ - simlo
##################################
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time process_radtags -f /home/iovercast/manuscript-analysis/simulated_data/simlo/simlo_R1_.fastq.gz -i gzfastq -b /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/stacks_barcodes.txt -e pstI -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo; time denovo_map.pl -T 40 -b 1 -S  -m 2 -M 10 -N 10 -n 10  -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo --samples /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -O /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/stacks_popmap.txt
Processing single-end data.
Using Phred+33 encoding for quality scores.
Found 1 input file(s).
Searching for single-end, inlined barcodes.
Loaded 12 barcodes (9bp).
Processing file 1 of 1 [simlo_R1_.fastq.gz]
  2397592 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 2397592 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/process_radtags.log'

2397592 total sequences;
  0 ambiguous barcode drops;
  0 low quality read drops;
  0 ambiguous RAD-Tag drops;
2397592 retained reads.

real	0m14.472s
user	0m14.309s
sys	0m0.020s
Parsed population map: 12 files in 1 population and 1 group.
Found 12 sample file(s).
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1A_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 1 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   1 of  12 [1A_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1B_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 2 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   2 of  12 [1B_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1C_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 3 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   3 of  12 [1C_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1D_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 4 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   4 of  12 [1D_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2E_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 5 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   5 of  12 [2E_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2F_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 6 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   6 of  12 [2F_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2G_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 7 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   7 of  12 [2G_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2H_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 8 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   8 of  12 [2H_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3I_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 9 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   9 of  12 [3I_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3J_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 10 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file  10 of  12 [3J_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3K_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 11 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file  11 of  12 [3K_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3L_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -i 12 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file  12 of  12 [3L_0]

Depths of Coverage for Processed Samples:
1A_0: 19.924x
1B_0: 19.9052x
1C_0: 19.9236x
1D_0: 19.906x
2E_0: 19.9419x
2F_0: 19.8546x
2G_0: 19.8844x
2H_0: 19.8748x
3I_0: 19.8683x
3J_0: 19.8589x
3K_0: 19.8598x
3L_0: 19.9236x

Generating catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/cstacks -b 1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3L_0  -p 40 -n 10 2>&1
Matching samples to the catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/sstacks -b 1 -c /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/batch_1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/3L_0  -p 40 2>&1
Calculating population-level summary statistics
/home/iovercast/manuscript-analysis/miniconda/bin/populations -b 1 -P /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo -s -t 40 --vcf --genepop --structure --phase --fastphase --phylip  -M /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simlo/stacks_popmap.txt 2>&1

real	1m49.086s
user	12m2.639s
sys	0m4.565s

##################################
Doing - /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/ - simhi
##################################
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time process_radtags -f /home/iovercast/manuscript-analysis/simulated_data/simhi/simhi_R1_.fastq.gz -i gzfastq -b /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/stacks_barcodes.txt -e pstI -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi; time denovo_map.pl -T 40 -b 1 -S  -m 2 -M 10 -N 10 -n 10  -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi --samples /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -O /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/stacks_popmap.txt
Processing single-end data.
Using Phred+33 encoding for quality scores.
Found 1 input file(s).
Searching for single-end, inlined barcodes.
Loaded 12 barcodes (9bp).
Processing file 1 of 1 [simhi_R1_.fastq.gz]
  2400054 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 2400054 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/process_radtags.log'

2400054 total sequences;
  0 ambiguous barcode drops;
  0 low quality read drops;
  0 ambiguous RAD-Tag drops;
2400054 retained reads.

real	0m16.147s
user	0m15.936s
sys	0m0.031s
Parsed population map: 12 files in 1 population and 1 group.
Found 12 sample file(s).
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1A_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 1 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   1 of  12 [1A_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1B_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 2 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   2 of  12 [1B_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1C_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 3 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   3 of  12 [1C_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1D_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 4 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   4 of  12 [1D_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2E_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 5 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   5 of  12 [2E_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2F_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 6 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   6 of  12 [2F_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2G_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 7 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   7 of  12 [2G_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2H_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 8 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   8 of  12 [2H_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3I_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 9 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file   9 of  12 [3I_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3J_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 10 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file  10 of  12 [3J_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3K_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 11 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file  11 of  12 [3K_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3L_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -i 12 -r -m 2 -p 40 -M 10 -N 10 2>&1
Identifying unique stacks; file  12 of  12 [3L_0]

Depths of Coverage for Processed Samples:
1A_0: 19.8407x
1B_0: 19.8289x
1C_0: 19.9126x
1D_0: 19.9053x
2E_0: 19.8216x
2F_0: 19.8679x
2G_0: 19.8422x
2H_0: 19.8448x
3I_0: 19.7883x
3J_0: 19.7765x
3K_0: 19.8268x
3L_0: 19.8712x

Generating catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/cstacks -b 1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3L_0  -p 40 -n 10 2>&1
Matching samples to the catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/sstacks -b 1 -c /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/batch_1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/3L_0  -p 40 2>&1
Calculating population-level summary statistics
/home/iovercast/manuscript-analysis/miniconda/bin/populations -b 1 -P /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi -s -t 40 --vcf --genepop --structure --phase --fastphase --phylip  -M /home/iovercast/manuscript-analysis/stacks/SIMDATA/ungapped/simhi/stacks_popmap.txt 2>&1

real	1m53.780s
user	12m1.654s
sys	0m5.007s

##################################
Doing - /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/ - simno
##################################
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time process_radtags -f /home/iovercast/manuscript-analysis/simulated_data/simno/simno_R1_.fastq.gz -i gzfastq -b /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/stacks_barcodes.txt -e pstI -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno; time denovo_map.pl -T 40 -b 1 -S  -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno --samples /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -O /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/stacks_popmap.txt
Processing single-end data.
Using Phred+33 encoding for quality scores.
Found 1 input file(s).
Searching for single-end, inlined barcodes.
Loaded 12 barcodes (9bp).
Processing file 1 of 1 [simno_R1_.fastq.gz]
  2398782 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 2398782 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/process_radtags.log'

2398782 total sequences;
  0 ambiguous barcode drops;
  0 low quality read drops;
  0 ambiguous RAD-Tag drops;
2398782 retained reads.

real	0m14.677s
user	0m14.512s
sys	0m0.025s
Parsed population map: 12 files in 1 population and 1 group.
Found 12 sample file(s).
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1A_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 1 -r  -p 40 2>&1
Identifying unique stacks; file   1 of  12 [1A_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1B_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 2 -r  -p 40 2>&1
Identifying unique stacks; file   2 of  12 [1B_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1C_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 3 -r  -p 40 2>&1
Identifying unique stacks; file   3 of  12 [1C_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1D_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 4 -r  -p 40 2>&1
Identifying unique stacks; file   4 of  12 [1D_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2E_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 5 -r  -p 40 2>&1
Identifying unique stacks; file   5 of  12 [2E_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2F_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 6 -r  -p 40 2>&1
Identifying unique stacks; file   6 of  12 [2F_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2G_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 7 -r  -p 40 2>&1
Identifying unique stacks; file   7 of  12 [2G_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2H_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 8 -r  -p 40 2>&1
Identifying unique stacks; file   8 of  12 [2H_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3I_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 9 -r  -p 40 2>&1
Identifying unique stacks; file   9 of  12 [3I_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3J_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 10 -r  -p 40 2>&1
Identifying unique stacks; file  10 of  12 [3J_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3K_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 11 -r  -p 40 2>&1
Identifying unique stacks; file  11 of  12 [3K_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3L_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -i 12 -r  -p 40 2>&1
Identifying unique stacks; file  12 of  12 [3L_0]

Depths of Coverage for Processed Samples:
1A_0: 19.9051x
1B_0: 19.9106x
1C_0: 19.9199x
1D_0: 19.9458x
2E_0: 19.8817x
2F_0: 19.8906x
2G_0: 19.9295x
2H_0: 19.9191x
3I_0: 19.8735x
3J_0: 19.8835x
3K_0: 19.8506x
3L_0: 19.9288x

Generating catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/cstacks -b 1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3L_0  -p 40 2>&1
Matching samples to the catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/sstacks -b 1 -c /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/batch_1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/3L_0  -p 40 2>&1
Calculating population-level summary statistics
/home/iovercast/manuscript-analysis/miniconda/bin/populations -b 1 -P /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno -s -t 40 --vcf --genepop --structure --phase --fastphase --phylip  -M /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simno/stacks_popmap.txt 2>&1

real	1m52.769s
user	3m2.639s
sys	0m4.437s

##################################
Doing - /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/ - simlo
##################################
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time process_radtags -f /home/iovercast/manuscript-analysis/simulated_data/simlo/simlo_R1_.fastq.gz -i gzfastq -b /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/stacks_barcodes.txt -e pstI -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo; time denovo_map.pl -T 40 -b 1 -S  -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo --samples /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -O /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/stacks_popmap.txt
Processing single-end data.
Using Phred+33 encoding for quality scores.
Found 1 input file(s).
Searching for single-end, inlined barcodes.
Loaded 12 barcodes (9bp).
Processing file 1 of 1 [simlo_R1_.fastq.gz]
  2397592 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 2397592 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/process_radtags.log'

2397592 total sequences;
  0 ambiguous barcode drops;
  0 low quality read drops;
  0 ambiguous RAD-Tag drops;
2397592 retained reads.

real	0m15.063s
user	0m14.907s
sys	0m0.027s
Parsed population map: 12 files in 1 population and 1 group.
Found 12 sample file(s).
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1A_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 1 -r  -p 40 2>&1
Identifying unique stacks; file   1 of  12 [1A_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1B_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 2 -r  -p 40 2>&1
Identifying unique stacks; file   2 of  12 [1B_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1C_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 3 -r  -p 40 2>&1
Identifying unique stacks; file   3 of  12 [1C_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1D_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 4 -r  -p 40 2>&1
Identifying unique stacks; file   4 of  12 [1D_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2E_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 5 -r  -p 40 2>&1
Identifying unique stacks; file   5 of  12 [2E_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2F_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 6 -r  -p 40 2>&1
Identifying unique stacks; file   6 of  12 [2F_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2G_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 7 -r  -p 40 2>&1
Identifying unique stacks; file   7 of  12 [2G_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2H_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 8 -r  -p 40 2>&1
Identifying unique stacks; file   8 of  12 [2H_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3I_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 9 -r  -p 40 2>&1
Identifying unique stacks; file   9 of  12 [3I_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3J_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 10 -r  -p 40 2>&1
Identifying unique stacks; file  10 of  12 [3J_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3K_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 11 -r  -p 40 2>&1
Identifying unique stacks; file  11 of  12 [3K_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3L_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -i 12 -r  -p 40 2>&1
Identifying unique stacks; file  12 of  12 [3L_0]

Depths of Coverage for Processed Samples:
1A_0: 19.8703x
1B_0: 19.8456x
1C_0: 19.8661x
1D_0: 19.8248x
2E_0: 19.8685x
2F_0: 19.7992x
2G_0: 19.8052x
2H_0: 19.8035x
3I_0: 19.8049x
3J_0: 19.8094x
3K_0: 19.7808x
3L_0: 19.8502x

Generating catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/cstacks -b 1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3L_0  -p 40 2>&1
Matching samples to the catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/sstacks -b 1 -c /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/batch_1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/3L_0  -p 40 2>&1
Calculating population-level summary statistics
/home/iovercast/manuscript-analysis/miniconda/bin/populations -b 1 -P /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo -s -t 40 --vcf --genepop --structure --phase --fastphase --phylip  -M /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simlo/stacks_popmap.txt 2>&1

real	1m53.102s
user	3m3.499s
sys	0m5.124s

##################################
Doing - /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/ - simhi
##################################
export PATH=/home/iovercast/manuscript-analysis//miniconda/bin:$PATH; time process_radtags -f /home/iovercast/manuscript-analysis/simulated_data/simhi/simhi_R1_.fastq.gz -i gzfastq -b /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/stacks_barcodes.txt -e pstI -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi; time denovo_map.pl -T 40 -b 1 -S  -X 'populations:--vcf --genepop --structure --phase --fastphase --phylip ' -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi --samples /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -O /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/stacks_popmap.txt
Processing single-end data.
Using Phred+33 encoding for quality scores.
Found 1 input file(s).
Searching for single-end, inlined barcodes.
Loaded 12 barcodes (9bp).
Processing file 1 of 1 [simhi_R1_.fastq.gz]
  2400054 total reads; -0 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 2400054 retained reads.
Closing files, flushing buffers...
Outputing details to log: '/home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/process_radtags.log'

2400054 total sequences;
  0 ambiguous barcode drops;
  0 low quality read drops;
  0 ambiguous RAD-Tag drops;
2400054 retained reads.

real	0m14.688s
user	0m14.534s
sys	0m0.024s
Parsed population map: 12 files in 1 population and 1 group.
Found 12 sample file(s).
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1A_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 1 -r  -p 40 2>&1
Identifying unique stacks; file   1 of  12 [1A_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1B_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 2 -r  -p 40 2>&1
Identifying unique stacks; file   2 of  12 [1B_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1C_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 3 -r  -p 40 2>&1
Identifying unique stacks; file   3 of  12 [1C_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1D_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 4 -r  -p 40 2>&1
Identifying unique stacks; file   4 of  12 [1D_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2E_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 5 -r  -p 40 2>&1
Identifying unique stacks; file   5 of  12 [2E_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2F_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 6 -r  -p 40 2>&1
Identifying unique stacks; file   6 of  12 [2F_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2G_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 7 -r  -p 40 2>&1
Identifying unique stacks; file   7 of  12 [2G_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2H_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 8 -r  -p 40 2>&1
Identifying unique stacks; file   8 of  12 [2H_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3I_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 9 -r  -p 40 2>&1
Identifying unique stacks; file   9 of  12 [3I_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3J_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 10 -r  -p 40 2>&1
Identifying unique stacks; file  10 of  12 [3J_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3K_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 11 -r  -p 40 2>&1
Identifying unique stacks; file  11 of  12 [3K_0]
  /home/iovercast/manuscript-analysis/miniconda/bin/ustacks -t gzfastq -f /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3L_0.fq.gz -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -i 12 -r  -p 40 2>&1
Identifying unique stacks; file  12 of  12 [3L_0]

Depths of Coverage for Processed Samples:
1A_0: 19.7736x
1B_0: 19.7582x
1C_0: 19.8454x
1D_0: 19.8244x
2E_0: 19.7413x
2F_0: 19.801x
2G_0: 19.7575x
2H_0: 19.7719x
3I_0: 19.7156x
3J_0: 19.7059x
3K_0: 19.752x
3L_0: 19.8041x

Generating catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/cstacks -b 1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3L_0  -p 40 2>&1
Matching samples to the catalog...
  /home/iovercast/manuscript-analysis/miniconda/bin/sstacks -b 1 -c /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/batch_1 -o /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1A_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1B_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1C_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/1D_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2E_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2F_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2G_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/2H_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3I_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3J_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3K_0 -s /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/3L_0  -p 40 2>&1
Calculating population-level summary statistics
/home/iovercast/manuscript-analysis/miniconda/bin/populations -b 1 -P /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi -s -t 40 --vcf --genepop --structure --phase --fastphase --phylip  -M /home/iovercast/manuscript-analysis/stacks/SIMDATA/default/simhi/stacks_popmap.txt 2>&1

real	1m55.680s
user	3m6.456s
sys	0m5.915s

aftrRAD simulated data assembly

aftrRAD throws out any read with one or more bases less than the phred qscore minQual setting. You can't really tune how many low quality bases to retain. For the simulated data we are simulating all qscores arbitrarily high, so this isn't a problem. For empirical we might have to think about lowering minQual...

Actually, throwing out many reads seems to be the aftrRAD strategy. I think its trying to reduce the number of potential reads to match (reduce singletons from error) because it

Performance on 10000 100bp simulated dataset:

  • ~200 minutes

Performance on 100000 100bp simulated dataset:

  • AftrRad.pl - ~4500 minutes
  • Genotype.pl - 13 days (my notebook crashed, but it finished in about this long)
In [ ]:
import subprocess
import gzip

## Set up directory structures. change the force flag if you want to
## blow everything away and restart
# force = True
force = ""
AFTRRAD_SIMOUT=os.path.join(AFTRRAD_DIR, "SIMDATA/")
if force and os.path.exists(AFTRRAD_SIMOUT):
    shutil.rmtree(AFTRRAD_SIMOUT)
if not os.path.exists(AFTRRAD_SIMOUT):
    os.makedirs(AFTRRAD_SIMOUT)
for outdir in ["no/", "lo/", "hi/", "large/"]:
    tmpdir = os.path.join(AFTRRAD_SIMOUT, "sim"+outdir)
    if not os.path.exists(tmpdir):
        os.makedirs(tmpdir)

## go to the pyrad simulated data output directory
for dir in ["no", "lo", "hi", "large"]:
    print("Doing - {}".format(dir))
    ## Set barcode and raw data files
    simdata_dir = os.path.join(SIMULATION_DATA_DIR, "sim"+dir)
    ipyrad_bcodes = os.path.join(simdata_dir, "sim{}_barcodes.txt".format(dir))
    fastqs = os.path.join(simdata_dir, "sim{}_R1_.fastq.gz".format(dir))

    simout_dir = os.path.join(AFTRRAD_SIMOUT, "sim"+dir)
    if not os.path.exists(simout_dir):
        os.mkdir(simout_dir)
    bcodes = os.path.join(simout_dir, "aftrrad-{}-barcodes.txt".format(dir))
    ## Munge the ipyrad barcodes file to the format aftrrad wants
    ## (barcode\tsample name)
    with open(ipyrad_bcodes, 'r') as infile:
        with open(bcodes, 'w') as outfile:
            lines = infile.readlines()
            for line in lines:
                if line:
                    outfile.write("\t".join(line.split()[::-1])+"\n")

    ## Make data and barcodes directories
    data_dir = os.path.join(simout_dir, "Data")
    bcodes_dir = os.path.join(simout_dir, "Barcodes")
    for tmp in [data_dir, bcodes_dir]:
        if not os.path.exists(tmp):
            os.mkdir(tmp)
    ## Copy the fastq to the aftrrad/Data dir and the barcodes to the
    ## aftrrad/Barcodes dir. These files have to be in these directories
    ## and they have to have the exact same name, derp.
    aftrrad_fastqs = os.path.join(data_dir, "sim-{}.txt".format(dir))
    with gzip.open(fastqs, 'rb') as f_in, open(aftrrad_fastqs, 'wb') as f_out:
        shutil.copyfileobj(f_in, f_out)
    shutil.copy2(bcodes, os.path.join(bcodes_dir, "sim-{}.txt".format(dir)))
    
    ## AfterRAD is incredibly picky about where scripts and binaries are so you
    ## have to do a bunch of annoying housekeeping.
    cmd = "cp -rf {}/* {}".format(os.path.join(AFTRRAD_DIR, "AftrRAD/AftrRADv5.0"), simout_dir)
    os.system(cmd)
    shutil.copy2(os.path.join(AFTRRAD_DIR, "dnaMatrix"), simout_dir)
    shutil.copy2(os.path.join(AFTRRAD_DIR, "ACANA"), simout_dir)

    ## This first line of nonsense is to make it so perl can find the Parallel::ForkManager library
    base = "export PATH={}perl5/bin:$PATH; cpanm --local-lib={}/perl5 local::lib && eval $(perl -I {}/perl5/lib/perl5/ -Mlocal::lib); ".format(WORK_DIR, WORK_DIR, WORK_DIR)

    ## Good sub for testing
    cmd = base + "time perl AftrRAD.pl -h"

    ## numIndels-3 What do here?
    ## stringLength-99 We don't care about homoplymers here, so set it very high
    ## maxH-90 ??
    ## AftrRAD manu analysis settings - P2: noP2;  minDepth: 5; numIndel: 3; MinReads: 5
    cmd = base + "time perl AftrRAD.pl re-TGCAG minDepth-6 P2-noP2 minIden-85 " \
               + "stringLength-99" \
               + "DataPath-Data/ BarcodePath-Barcodes/ maxProcesses-40"
    os.chdir(simout_dir)
    print(cmd)
    output = ""
    try:
        output = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT)
        pass
    except Exception as inst:
        print(inst.output)
    print(output)

    ## MinReads is mindepth_statistical
    cmd = base + "time perl Genotype.pl MinReads-6 subset-0 maxProcesses-40"
    #cmd = base + "perl Genotype.pl -h"
    print(cmd)
    output = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT)
    print(output)

    ## pctScored is min_samples_locus as a percent of total samples, here since
    ##    we use 2 for min_samples_locus and there are 12 simulated samples we use 17%
    cmd = base + "time perl FilterSNPs.pl pctScored-17"
    print(cmd)
    output = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT)
    print(output)
Doing - no
export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl AftrRAD.pl re-TGCAG minDepth-6 P2-noP2 minIden-85 stringLength-99DataPath-Data/ BarcodePath-Barcodes/ maxProcesses-40
local::lib is up to date. (2.000019)


Arguments entered are...
minParalog	5
minDepth	6
MaxH	90
P2	noP2
BarcodePath	Barcodes/
minQual	20
re	TGCAG
numIndels	3
Phred	33
minIden	85
maxProcesses	40
stringLength	99DataPath
dplexedData	0
Help	0
DataPath	Data/


Running AftrRAD...

Recognized 1 data files.

File names are...
 sim-no.txt 

Use of uninitialized value $TotalBarcodeNonMatches in concatenation (.) or string at AftrRAD.pl line 1072.
Use of uninitialized value $TotalBarcodeNonMatches in concatenation (.) or string at AftrRAD.pl line 1073.
The barcodes you entered for data file 0.0 (file sim-no.txt) are...
 CATCATCAT TCAACTCTC AATACTAGT GAGTGACAG ATGGACCTT CGAGTTTCC TGTTAATAA TCCGTAGCC GTTTCAATC AGAATCTGC AATCGCCGT AGTCCGCTA 

The names you entered for data file 0.0 (file sim-no.txt) are...
 1A_0 1B_0 1C_0 1D_0 2E_0 2F_0 2G_0 2H_0 3I_0 3J_0 3K_0 3L_0 


Demultiplexing samples for data file sim-no.txt.

Identifying unique sequences for each individual.
23741 TempFiles/SubTemp_0/UniqueWithCountsIndividual1A_0.txt
23790 TempFiles/SubTemp_0/UniqueWithCountsIndividual1B_0.txt
23981 TempFiles/SubTemp_0/UniqueWithCountsIndividual1C_0.txt
23890 TempFiles/SubTemp_0/UniqueWithCountsIndividual1D_0.txt
23919 TempFiles/SubTemp_0/UniqueWithCountsIndividual2E_0.txt
23925 TempFiles/SubTemp_0/UniqueWithCountsIndividual2F_0.txt
24022 TempFiles/SubTemp_0/UniqueWithCountsIndividual2G_0.txt
23860 TempFiles/SubTemp_0/UniqueWithCountsIndividual2H_0.txt
23843 TempFiles/SubTemp_0/UniqueWithCountsIndividual3I_0.txt
23709 TempFiles/SubTemp_0/UniqueWithCountsIndividual3J_0.txt
23703 TempFiles/SubTemp_0/UniqueWithCountsIndividual3K_0.txt
23986 TempFiles/SubTemp_0/UniqueWithCountsIndividual3L_0.txt

Identifying all unique sequences within the dataset.

Creating file to test mean read counts.
Testing nonzero means in read counts to identify error reads.

Performing heuristic search of all pairwise comparisons to identify potentially allelic pairs.
Rapidly searching unique sequence number 1000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 2000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 3000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 4000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 5000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 6000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 7000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 8000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 9000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 10000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 11000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 12000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 13000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 14000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 15000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 16000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 17000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 18000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 19000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 20000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 21000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 22000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 23000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 24000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 25000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 26000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 27000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 28000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 29000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 30000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 31000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 32000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 33000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 34000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 35000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 36000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 37000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 38000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 39000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 40000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 41000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 42000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 43000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 44000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 45000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 46000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 47000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 48000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 49000 of 50695 for potentially allelic read pairs.
Rapidly searching unique sequence number 50000 of 50695 for potentially allelic read pairs.

Number of pairwise comparisons to align and evaluate is 117495
Working on alignment 40000 of 117495.
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Working on alignment 80000 of 117495.
Working on alignment 80000 of 117495.
Working on alignment 80000 of 117495.

Scoring each pairwise alignment.  Alignments exceeding 85 % similarity will be retained.
Parsing aligned sequences into candidate loci.
Working on alignment 4000 of 9958.
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Working on alignment 8000 of 9958.
Finished writing the mafft output.
Identifying and removing paralogous loci.


Loci have been identified.  Aligned polymorphic loci are stored in the Output directory.  Read counts for the alleles at these loci can be found for each individual in the files stored in TempFiles/RawReadCountFiles.

Demultiplexing and other general information can be found for each dataset analyzed in the Output/RunInfo directory.

Next, run Genotype.pl, followed by FilterSNPs.pl to genotype all individuals and output SNPs for subsequent analyses.


real	53m20.317s
user	57m14.741s
sys	30m25.360s

export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl Genotype.pl MinReads-6 subset-0 maxProcesses-40
local::lib is up to date. (2.000019)


Arguments entered are...
subsetfile	SamplesForSubset.txt
pvalLow	0.0001
pvalThresh	100
subset	0
maxProcesses	40
MinReads	6
pvalHigh	1e-05
Help	0


Running Genotype.pl...

Scoring genotypes at all nonparalogous loci.

Currently genotyping sample...1C_0	1B_0	2F_0	3L_0	3I_0	2G_0	1A_0	2H_0	3K_0	1D_0	2E_0	3J_0	Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
cat: TempFiles/SubGenotypes_12/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_13/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_14/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_15/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_16/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_17/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_18/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_19/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_20/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_21/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_22/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_23/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_24/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_25/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_26/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_27/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_28/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_29/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_30/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_31/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_32/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_33/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_34/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_35/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_36/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_37/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_38/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_39/SubGenotypes.txt: No such file or directory
Creating SNPMatrixAll from R Script


Checking for individuals with large amounts of missing data (have >2 StDev more missing data than the average)
Identifying samples with >2 stdev missing data
Read 12 items
Read 12 items
null device 
          1 
No samples were flagged as potentially bad samples.  Would like to remove any samples from further analyses anyway? (y/n)
All individuals will be analyzed.
All samples were included in analyses.
Reading SNPMatrixAll file
Identifying monomorphic loci
123 TempFiles/MonomorphicsNoParalogs.txt
Updating Genotypes.txt file

Identifying SNPs and determining the position of each SNP along the read.
Plotting SNP locations
Read 43744 items

Loci have all been genotyped, and scored genotypes are stored in the file 'Genotypes.txt' in the TempFiles folder.

The locations of each SNP are plotted in the file SNPLocations.pdf in the Output/RunInfo folder.  Use this plot to choose a cut-off value for omitting SNPs due to artifacts toward the ends of reads.

Next, run 'FilterSNPs.pl' to filter and output SNPs and monomorphic loci based on 1.) the proportion of samples genotyped at each locus and 2.) SNP positions along the reads.

real	132m18.179s
user	133m10.479s
sys	0m27.222s

export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl FilterSNPs.pl pctScored-17
local::lib is up to date. (2.000019)


Arguments entered are...
maxSNP	0
MinReads	6
pctScored	17
Help	0


Running FilterSNPs.pl...

Identifying all SNPs that are scored in 17% of the samples
Individual SNPs, haplotypes, and monomorphic loci have been printed to files located in Output/Genotypes.
These data can be further formatted using the scripts in the 'Formatting' directory

real	17m35.580s
user	17m35.781s
sys	0m0.360s

Doing - lo
export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl AftrRAD.pl re-TGCAG minDepth-6 P2-noP2 minIden-85 stringLength-99DataPath-Data/ BarcodePath-Barcodes/ maxProcesses-40
local::lib is up to date. (2.000019)


Arguments entered are...
minParalog	5
minDepth	6
MaxH	90
P2	noP2
BarcodePath	Barcodes/
minQual	20
re	TGCAG
numIndels	3
Phred	33
minIden	85
maxProcesses	40
stringLength	99DataPath
dplexedData	0
Help	0
DataPath	Data/


Running AftrRAD...

Recognized 1 data files.

File names are...
 sim-lo.txt 

Use of uninitialized value $TotalBarcodeNonMatches in concatenation (.) or string at AftrRAD.pl line 1072.
Use of uninitialized value $TotalBarcodeNonMatches in concatenation (.) or string at AftrRAD.pl line 1073.
The barcodes you entered for data file 0.0 (file sim-lo.txt) are...
 CATCATCAT TCAACTCTC AATACTAGT GAGTGACAG ATGGACCTT CGAGTTTCC TGTTAATAA TCCGTAGCC GTTTCAATC AGAATCTGC AATCGCCGT AGTCCGCTA 

The names you entered for data file 0.0 (file sim-lo.txt) are...
 1A_0 1B_0 1C_0 1D_0 2E_0 2F_0 2G_0 2H_0 3I_0 3J_0 3K_0 3L_0 


Demultiplexing samples for data file sim-lo.txt.

Identifying unique sequences for each individual.
23715 TempFiles/SubTemp_0/UniqueWithCountsIndividual1A_0.txt
23787 TempFiles/SubTemp_0/UniqueWithCountsIndividual1B_0.txt
23816 TempFiles/SubTemp_0/UniqueWithCountsIndividual1C_0.txt
23743 TempFiles/SubTemp_0/UniqueWithCountsIndividual1D_0.txt
23753 TempFiles/SubTemp_0/UniqueWithCountsIndividual2E_0.txt
23828 TempFiles/SubTemp_0/UniqueWithCountsIndividual2F_0.txt
23969 TempFiles/SubTemp_0/UniqueWithCountsIndividual2G_0.txt
23582 TempFiles/SubTemp_0/UniqueWithCountsIndividual2H_0.txt
23847 TempFiles/SubTemp_0/UniqueWithCountsIndividual3I_0.txt
23707 TempFiles/SubTemp_0/UniqueWithCountsIndividual3J_0.txt
24032 TempFiles/SubTemp_0/UniqueWithCountsIndividual3K_0.txt
23685 TempFiles/SubTemp_0/UniqueWithCountsIndividual3L_0.txt

Identifying all unique sequences within the dataset.

Creating file to test mean read counts.
Testing nonzero means in read counts to identify error reads.

Performing heuristic search of all pairwise comparisons to identify potentially allelic pairs.
Rapidly searching unique sequence number 1000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 2000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 3000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 4000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 5000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 6000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 7000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 8000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 9000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 10000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 11000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 12000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 13000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 14000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 15000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 16000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 17000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 18000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 19000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 20000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 21000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 22000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 23000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 24000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 25000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 26000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 27000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 28000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 29000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 30000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 31000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 32000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 33000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 34000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 35000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 36000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 37000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 38000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 39000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 40000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 41000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 42000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 43000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 44000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 45000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 46000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 47000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 48000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 49000 of 50709 for potentially allelic read pairs.
Rapidly searching unique sequence number 50000 of 50709 for potentially allelic read pairs.

Number of pairwise comparisons to align and evaluate is 117112
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
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Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 40000 of 117112.
Working on alignment 80000 of 117112.
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Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.
Working on alignment 80000 of 117112.

Scoring each pairwise alignment.  Alignments exceeding 85 % similarity will be retained.
Parsing aligned sequences into candidate loci.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
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Working on alignment 4000 of 9983.
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Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
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Working on alignment 4000 of 9983.
Working on alignment 4000 of 9983.
Working on alignment 8000 of 9983.
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Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Working on alignment 8000 of 9983.
Finished writing the mafft output.
Identifying and removing paralogous loci.


Loci have been identified.  Aligned polymorphic loci are stored in the Output directory.  Read counts for the alleles at these loci can be found for each individual in the files stored in TempFiles/RawReadCountFiles.

Demultiplexing and other general information can be found for each dataset analyzed in the Output/RunInfo directory.

Next, run Genotype.pl, followed by FilterSNPs.pl to genotype all individuals and output SNPs for subsequent analyses.


real	54m2.709s
user	58m11.067s
sys	29m20.879s

export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl Genotype.pl MinReads-6 subset-0 maxProcesses-40
local::lib is up to date. (2.000019)


Arguments entered are...
subsetfile	SamplesForSubset.txt
pvalLow	0.0001
pvalThresh	100
subset	0
maxProcesses	40
MinReads	6
pvalHigh	1e-05
Help	0


Running Genotype.pl...

Scoring genotypes at all nonparalogous loci.

Currently genotyping sample...1C_0	1B_0	1D_0	2E_0	1A_0	3K_0	3I_0	3J_0	2G_0	2F_0	2H_0	3L_0	Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
cat: TempFiles/SubGenotypes_12/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_13/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_14/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_15/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_16/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_17/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_18/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_19/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_20/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_21/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_22/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_23/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_24/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_25/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_26/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_27/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_28/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_29/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_30/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_31/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_32/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_33/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_34/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_35/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_36/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_37/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_38/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_39/SubGenotypes.txt: No such file or directory
Creating SNPMatrixAll from R Script


Checking for individuals with large amounts of missing data (have >2 StDev more missing data than the average)
Identifying samples with >2 stdev missing data
Read 12 items
Read 12 items
null device 
          1 


Samples identified as potentially bad samples are "Individual2H_0".

Do you want to remove all(a), some(s), or none(n) of these potentially bad samples from the analysis? (a/s/n)
All flagged samples will be retained for analyses.
Are there any additional samples you would like to remove from the analysis? (y/n)
All samples were included in analyses.
Reading SNPMatrixAll file
Identifying monomorphic loci
157 TempFiles/MonomorphicsNoParalogs.txt
Updating Genotypes.txt file

Identifying SNPs and determining the position of each SNP along the read.
Plotting SNP locations
Read 43178 items

Loci have all been genotyped, and scored genotypes are stored in the file 'Genotypes.txt' in the TempFiles folder.

The locations of each SNP are plotted in the file SNPLocations.pdf in the Output/RunInfo folder.  Use this plot to choose a cut-off value for omitting SNPs due to artifacts toward the ends of reads.

Next, run 'FilterSNPs.pl' to filter and output SNPs and monomorphic loci based on 1.) the proportion of samples genotyped at each locus and 2.) SNP positions along the reads.

real	130m1.750s
user	130m40.646s
sys	0m36.565s

export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl FilterSNPs.pl pctScored-17
local::lib is up to date. (2.000019)


Arguments entered are...
maxSNP	0
MinReads	6
pctScored	17
Help	0


Running FilterSNPs.pl...

Identifying all SNPs that are scored in 17% of the samples
Individual SNPs, haplotypes, and monomorphic loci have been printed to files located in Output/Genotypes.
These data can be further formatted using the scripts in the 'Formatting' directory

real	16m30.922s
user	16m30.948s
sys	0m0.567s

Doing - hi
export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl AftrRAD.pl re-TGCAG minDepth-6 P2-noP2 minIden-85 stringLength-99DataPath-Data/ BarcodePath-Barcodes/ maxProcesses-40
local::lib is up to date. (2.000019)


Arguments entered are...
minParalog	5
minDepth	6
MaxH	90
P2	noP2
BarcodePath	Barcodes/
minQual	20
re	TGCAG
numIndels	3
Phred	33
minIden	85
maxProcesses	40
stringLength	99DataPath
dplexedData	0
Help	0
DataPath	Data/


Running AftrRAD...

Recognized 1 data files.

File names are...
 sim-hi.txt 

Use of uninitialized value $TotalBarcodeNonMatches in concatenation (.) or string at AftrRAD.pl line 1072.
Use of uninitialized value $TotalBarcodeNonMatches in concatenation (.) or string at AftrRAD.pl line 1073.
The barcodes you entered for data file 0.0 (file sim-hi.txt) are...
 CATCATCAT TCAACTCTC AATACTAGT GAGTGACAG ATGGACCTT CGAGTTTCC TGTTAATAA TCCGTAGCC GTTTCAATC AGAATCTGC AATCGCCGT AGTCCGCTA 

The names you entered for data file 0.0 (file sim-hi.txt) are...
 1A_0 1B_0 1C_0 1D_0 2E_0 2F_0 2G_0 2H_0 3I_0 3J_0 3K_0 3L_0 


Demultiplexing samples for data file sim-hi.txt.

Identifying unique sequences for each individual.
23768 TempFiles/SubTemp_0/UniqueWithCountsIndividual1A_0.txt
23907 TempFiles/SubTemp_0/UniqueWithCountsIndividual1B_0.txt
23839 TempFiles/SubTemp_0/UniqueWithCountsIndividual1C_0.txt
23943 TempFiles/SubTemp_0/UniqueWithCountsIndividual1D_0.txt
23738 TempFiles/SubTemp_0/UniqueWithCountsIndividual2E_0.txt
24089 TempFiles/SubTemp_0/UniqueWithCountsIndividual2F_0.txt
23995 TempFiles/SubTemp_0/UniqueWithCountsIndividual2G_0.txt
23937 TempFiles/SubTemp_0/UniqueWithCountsIndividual2H_0.txt
23693 TempFiles/SubTemp_0/UniqueWithCountsIndividual3I_0.txt
23882 TempFiles/SubTemp_0/UniqueWithCountsIndividual3J_0.txt
24042 TempFiles/SubTemp_0/UniqueWithCountsIndividual3K_0.txt
23819 TempFiles/SubTemp_0/UniqueWithCountsIndividual3L_0.txt

Identifying all unique sequences within the dataset.

Creating file to test mean read counts.
Testing nonzero means in read counts to identify error reads.

Performing heuristic search of all pairwise comparisons to identify potentially allelic pairs.
Rapidly searching unique sequence number 1000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 2000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 3000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 4000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 5000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 6000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 7000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 8000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 9000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 10000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 11000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 12000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 13000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 14000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 15000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 16000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 17000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 18000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 19000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 20000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 21000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 22000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 23000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 24000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 25000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 26000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 27000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 28000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 29000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 30000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 31000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 32000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 33000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 34000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 35000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 36000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 37000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 38000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 39000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 40000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 41000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 42000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 43000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 44000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 45000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 46000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 47000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 48000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 49000 of 50632 for potentially allelic read pairs.
Rapidly searching unique sequence number 50000 of 50632 for potentially allelic read pairs.

Number of pairwise comparisons to align and evaluate is 115832
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 40000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.
Working on alignment 80000 of 115832.

Scoring each pairwise alignment.  Alignments exceeding 85 % similarity will be retained.
Parsing aligned sequences into candidate loci.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 4000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Working on alignment 8000 of 10000.
Finished writing the mafft output.
Identifying and removing paralogous loci.


Loci have been identified.  Aligned polymorphic loci are stored in the Output directory.  Read counts for the alleles at these loci can be found for each individual in the files stored in TempFiles/RawReadCountFiles.

Demultiplexing and other general information can be found for each dataset analyzed in the Output/RunInfo directory.

Next, run Genotype.pl, followed by FilterSNPs.pl to genotype all individuals and output SNPs for subsequent analyses.


real	51m21.871s
user	55m37.453s
sys	27m33.546s

export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl Genotype.pl MinReads-6 subset-0 maxProcesses-40
local::lib is up to date. (2.000019)


Arguments entered are...
subsetfile	SamplesForSubset.txt
pvalLow	0.0001
pvalThresh	100
subset	0
maxProcesses	40
MinReads	6
pvalHigh	1e-05
Help	0


Running Genotype.pl...

Scoring genotypes at all nonparalogous loci.

Currently genotyping sample...1B_0	1D_0	2F_0	1C_0	3L_0	3I_0	2H_0	2E_0	1A_0	2G_0	3K_0	3J_0	Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Running R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
Finished R
cat: TempFiles/SubGenotypes_12/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_13/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_14/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_15/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_16/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_17/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_18/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_19/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_20/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_21/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_22/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_23/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_24/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_25/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_26/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_27/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_28/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_29/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_30/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_31/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_32/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_33/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_34/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_35/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_36/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_37/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_38/SubGenotypes.txt: No such file or directory
cat: TempFiles/SubGenotypes_39/SubGenotypes.txt: No such file or directory
Creating SNPMatrixAll from R Script


Checking for individuals with large amounts of missing data (have >2 StDev more missing data than the average)
Identifying samples with >2 stdev missing data
Read 12 items
Read 12 items
null device 
          1 
No samples were flagged as potentially bad samples.  Would like to remove any samples from further analyses anyway? (y/n)
All individuals will be analyzed.
All samples were included in analyses.
Reading SNPMatrixAll file
Identifying monomorphic loci
316 TempFiles/MonomorphicsNoParalogs.txt
Updating Genotypes.txt file

Identifying SNPs and determining the position of each SNP along the read.
Plotting SNP locations
Read 42696 items

Loci have all been genotyped, and scored genotypes are stored in the file 'Genotypes.txt' in the TempFiles folder.

The locations of each SNP are plotted in the file SNPLocations.pdf in the Output/RunInfo folder.  Use this plot to choose a cut-off value for omitting SNPs due to artifacts toward the ends of reads.

Next, run 'FilterSNPs.pl' to filter and output SNPs and monomorphic loci based on 1.) the proportion of samples genotyped at each locus and 2.) SNP positions along the reads.

real	132m4.553s
user	132m49.467s
sys	0m31.332s

export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl FilterSNPs.pl pctScored-17
local::lib is up to date. (2.000019)


Arguments entered are...
maxSNP	0
MinReads	6
pctScored	17
Help	0


Running FilterSNPs.pl...

Identifying all SNPs that are scored in 17% of the samples
Individual SNPs, haplotypes, and monomorphic loci have been printed to files located in Output/Genotypes.
These data can be further formatted using the scripts in the 'Formatting' directory

real	16m55.382s
user	16m43.769s
sys	0m11.928s

Doing - large
export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl AftrRAD.pl re-TGCAG minDepth-6 P2-noP2 minIden-85 stringLength-99DataPath-Data/ BarcodePath-Barcodes/ maxProcesses-40
local::lib is up to date. (2.000019)


Arguments entered are...
minParalog	5
minDepth	6
MaxH	90
P2	noP2
BarcodePath	Barcodes/
minQual	20
re	TGCAG
numIndels	3
Phred	33
minIden	85
maxProcesses	40
stringLength	99DataPath
dplexedData	0
Help	0
DataPath	Data/


Running AftrRAD...

Recognized 1 data files.

File names are...
 sim-large.txt 

Use of uninitialized value $TotalBarcodeNonMatches in concatenation (.) or string at AftrRAD.pl line 1072.
Use of uninitialized value $TotalBarcodeNonMatches in concatenation (.) or string at AftrRAD.pl line 1073.
The barcodes you entered for data file 0.0 (file sim-large.txt) are...
 CATCATCAT TCAACTCTC AATACTAGT GAGTGACAG ATGGACCTT CGAGTTTCC TGTTAATAA TCCGTAGCC GTTTCAATC AGAATCTGC AATCGCCGT AGTCCGCTA 

The names you entered for data file 0.0 (file sim-large.txt) are...
 1A_0 1B_0 1C_0 1D_0 2E_0 2F_0 2G_0 2H_0 3I_0 3J_0 3K_0 3L_0 


Demultiplexing samples for data file sim-large.txt.

Identifying unique sequences for each individual.
230313 TempFiles/SubTemp_0/UniqueWithCountsIndividual1A_0.txt
230281 TempFiles/SubTemp_0/UniqueWithCountsIndividual1B_0.txt
230711 TempFiles/SubTemp_0/UniqueWithCountsIndividual1C_0.txt
230759 TempFiles/SubTemp_0/UniqueWithCountsIndividual1D_0.txt
230739 TempFiles/SubTemp_0/UniqueWithCountsIndividual2E_0.txt
230332 TempFiles/SubTemp_0/UniqueWithCountsIndividual2F_0.txt
230101 TempFiles/SubTemp_0/UniqueWithCountsIndividual2G_0.txt
230593 TempFiles/SubTemp_0/UniqueWithCountsIndividual2H_0.txt
230566 TempFiles/SubTemp_0/UniqueWithCountsIndividual3I_0.txt
230382 TempFiles/SubTemp_0/UniqueWithCountsIndividual3J_0.txt
230680 TempFiles/SubTemp_0/UniqueWithCountsIndividual3K_0.txt
231109 TempFiles/SubTemp_0/UniqueWithCountsIndividual3L_0.txt

Identifying all unique sequences within the dataset.

Creating file to test mean read counts.
Testing nonzero means in read counts to identify error reads.

Performing heuristic search of all pairwise comparisons to identify potentially allelic pairs.
Rapidly searching unique sequence number 1000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 2000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 3000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 4000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 5000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 6000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 7000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 8000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 9000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 10000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 11000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 12000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 13000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 14000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 15000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 16000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 17000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 18000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 19000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 20000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 21000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 22000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 23000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 24000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 25000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 26000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 27000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 28000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 29000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 30000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 31000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 32000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 33000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 34000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 35000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 36000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 37000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 38000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 39000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 40000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 41000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 42000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 43000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 44000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 45000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 46000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 47000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 48000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 49000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 50000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 51000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 52000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 53000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 54000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 55000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 56000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 57000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 58000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 59000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 60000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 61000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 62000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 63000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 64000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 65000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 66000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 67000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 68000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 69000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 70000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 71000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 72000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 73000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 74000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 75000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 76000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 77000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 78000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 79000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 80000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 81000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 82000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 83000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 84000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 85000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 86000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 87000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 88000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 89000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 90000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 91000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 92000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 93000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 94000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 95000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 96000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 97000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 98000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 99000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 100000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 101000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 102000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 103000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 104000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 105000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 106000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 107000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 108000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 109000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 110000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 111000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 112000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 113000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 114000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 115000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 116000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 117000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 118000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 119000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 120000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 121000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 122000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 123000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 124000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 125000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 126000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 127000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 128000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 129000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 130000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 131000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 132000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 133000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 134000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 135000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 136000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 137000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 138000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 139000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 140000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 141000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 142000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 143000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 144000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 145000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 146000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 147000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 148000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 149000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 150000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 151000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 152000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 153000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 154000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 155000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 156000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 157000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 158000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 159000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 160000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 161000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 162000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 163000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 164000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 165000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 166000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 167000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 168000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 169000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 170000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 171000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 172000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 173000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 174000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 175000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 176000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 177000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 178000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 179000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 180000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 181000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 182000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 183000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 184000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 185000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 186000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 187000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 188000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 189000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 190000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 191000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 192000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 193000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 194000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 195000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 196000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 197000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 198000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 199000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 200000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 201000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 202000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 203000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 204000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 205000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 206000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 207000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 208000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 209000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 210000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 211000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 212000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 213000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 214000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 215000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 216000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 217000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 218000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 219000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 220000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 221000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 222000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 223000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 224000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 225000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 226000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 227000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 228000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 229000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 230000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 231000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 232000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 233000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 234000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 235000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 236000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 237000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 238000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 239000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 240000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 241000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 242000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 243000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 244000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 245000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 246000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 247000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 248000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 249000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 250000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 251000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 252000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 253000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 254000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 255000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 256000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 257000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 258000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 259000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 260000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 261000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 262000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 263000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 264000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 265000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 266000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 267000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 268000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 269000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 270000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 271000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 272000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 273000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 274000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 275000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 276000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 277000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 278000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 279000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 280000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 281000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 282000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 283000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 284000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 285000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 286000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 287000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 288000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 289000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 290000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 291000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 292000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 293000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 294000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 295000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 296000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 297000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 298000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 299000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 300000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 301000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 302000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 303000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 304000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 305000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 306000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 307000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 308000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 309000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 310000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 311000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 312000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 313000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 314000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 315000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 316000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 317000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 318000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 319000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 320000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 321000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 322000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 323000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 324000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 325000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 326000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 327000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 328000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 329000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 330000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 331000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 332000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 333000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 334000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 335000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 336000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 337000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 338000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 339000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 340000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 341000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 342000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 343000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 344000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 345000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 346000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 347000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 348000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 349000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 350000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 351000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 352000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 353000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 354000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 355000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 356000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 357000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 358000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 359000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 360000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 361000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 362000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 363000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 364000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 365000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 366000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 367000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 368000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 369000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 370000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 371000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 372000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 373000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 374000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 375000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 376000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 377000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 378000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 379000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 380000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 381000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 382000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 383000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 384000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 385000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 386000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 387000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 388000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 389000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 390000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 391000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 392000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 393000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 394000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 395000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 396000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 397000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 398000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 399000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 400000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 401000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 402000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 403000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 404000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 405000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 406000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 407000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 408000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 409000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 410000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 411000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 412000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 413000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 414000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 415000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 416000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 417000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 418000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 419000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 420000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 421000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 422000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 423000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 424000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 425000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 426000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 427000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 428000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 429000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 430000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 431000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 432000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 433000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 434000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 435000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 436000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 437000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 438000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 439000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 440000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 441000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 442000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 443000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 444000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 445000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 446000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 447000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 448000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 449000 of 496426 for potentially allelic read pairs.
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Rapidly searching unique sequence number 452000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 453000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 454000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 455000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 456000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 457000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 458000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 459000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 460000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 461000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 462000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 463000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 464000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 465000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 466000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 467000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 468000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 469000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 470000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 471000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 472000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 473000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 474000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 475000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 476000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 477000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 478000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 479000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 480000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 481000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 482000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 483000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 484000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 485000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 486000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 487000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 488000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 489000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 490000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 491000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 492000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 493000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 494000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 495000 of 496426 for potentially allelic read pairs.
Rapidly searching unique sequence number 496000 of 496426 for potentially allelic read pairs.

Number of pairwise comparisons to align and evaluate is 1132044
Working on alignment 40000 of 1132044.
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Working on alignment 800000 of 1132044.
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Working on alignment 840000 of 1132044.
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Working on alignment 960000 of 1132044.
Working on alignment 960000 of 1132044.
Working on alignment 960000 of 1132044.
Working on alignment 960000 of 1132044.
Working on alignment 960000 of 1132044.
Working on alignment 960000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
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Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1000000 of 1132044.
Working on alignment 1040000 of 1132044.
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Working on alignment 1040000 of 1132044.
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Working on alignment 1040000 of 1132044.
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Working on alignment 1040000 of 1132044.
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Working on alignment 1040000 of 1132044.
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Working on alignment 1040000 of 1132044.
Working on alignment 1040000 of 1132044.
Working on alignment 1040000 of 1132044.
Working on alignment 1040000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1080000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.
Working on alignment 1120000 of 1132044.

Scoring each pairwise alignment.  Alignments exceeding 85 % similarity will be retained.
Parsing aligned sequences into candidate loci.
Working on alignment 4000 of 99096.
Working on alignment 4000 of 99096.
Working on alignment 4000 of 99096.
Working on alignment 4000 of 99096.
Working on alignment 4000 of 99096.
Working on alignment 4000 of 99096.
Working on alignment 4000 of 99096.
Working on alignment 4000 of 99096.
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Finished writing the mafft output.
Identifying and removing paralogous loci.


Loci have been identified.  Aligned polymorphic loci are stored in the Output directory.  Read counts for the alleles at these loci can be found for each individual in the files stored in TempFiles/RawReadCountFiles.

Demultiplexing and other general information can be found for each dataset analyzed in the Output/RunInfo directory.

Next, run Genotype.pl, followed by FilterSNPs.pl to genotype all individuals and output SNPs for subsequent analyses.


real	4544m8.832s
user	4421m44.062s
sys	1322m3.702s

export PATH=/home/iovercast/manuscript-analysis/perl5/bin:$PATH; cpanm --local-lib=/home/iovercast/manuscript-analysis//perl5 local::lib && eval $(perl -I /home/iovercast/manuscript-analysis//perl5/lib/perl5/ -Mlocal::lib); time perl Genotype.pl MinReads-6 subset-0 maxProcesses-40

Post-processing aftrrad

aftrrad doesn't provide vcf as output so we have to make it ourselves

Ooof. The OutputFasta.pl file has a SNPsOnly flag, but it doesn't output an alignment, so you can't use it. Also snp-sites doesn't convert ambiguity codes, so aftrRAD post processing is totally not writing out a good vcf.

In [ ]:
%%bash -s "$WORK_DIR" -s "$AFTRRAD_DIR"
export PATH="$1/miniconda/bin:$PATH"; export "WORK_DIR=$1"; export "AFTRRAD_DIR=$2"

cd $AFTRRAD_DIR
./brew/bin/brew tap homebrew/science
./brew/bin/brew install snp-sites

## Copy the R binary to the miniconda bin dir so it will be available
cp brew/Cellar/snp-sites/2.2.0/bin/snp-sites $WORK_DIR/miniconda/bin/

cd SIMDATA
for d in sim*;
do
    echo $d
    cd $d/Formatting
    perl OutputFasta.pl SNPsOnly-1 ambig-1
    snp-sites -v -o $d.vcf SNPMatrix_*.All.fasta
done

More post processing for aftrRAD

The weird way snp-sites codes missing data is actually as a ref or alt allele so we have to convert all the indel variants to actually look like this './.' to align with other vcf formats for the results analysis.

In [ ]:
import os
import shutil
AFTRRAD_SIMOUT=os.path.join(AFTRRAD_DIR, "SIMDATA/")
os.chdir(AFTRRAD_SIMOUT)
for outdir in ["simno", "simlo", "simhi", "simlarge"]:
    myvcf = "{}/Formatting/{}.vcf".format(outdir, outdir)
    print("Doing - myvcf")
    shutil.copy2(myvcf, myvcf+".bak")
    f = open(myvcf)
    lines = f.readlines()
    newlines = []
    for line in lines:
        if "#" in line:
            newlines.append(line.strip())
            continue
        dat = line.split()
        ref = dat[3]
        alt2 = ""
        try:
            alt2 = dat[4].split(",")[1]
        except:
            pass
        alt1 = dat[4].split(",")[0]
        if "*" in [ref, alt1, alt2]:
            idx = [ref, alt1, alt2].index("*")
            for i, val in enumerate(dat[9:]):
                if int(val) == idx:
                    dat[9+i] = "./."
            #print(dat)
        newlines.append("\t".join(dat))
    outfile = open(myvcf, 'w')
    outfile.write("\n".join(newlines))
['1', '154', '.', 'C', 'A,*', '.', '.', '.', 'GT', '0', '0', '0', '0', '1', '0', '0', '0', '0', '0', '0', './.']
['1', '155', '.', 'A', 'M,*', '.', '.', '.', 'GT', '0', '1', '0', '0', '0', '0', '0', '0', '0', '0', '0', './.']
['1', '156', '.', 'T', 'C,*', '.', '.', '.', 'GT', '0', '0', '0', '0', '1', '1', '1', '0', '0', '0', '0', './.']
['1', '1204', '.', 'C', '*,S', '.', '.', '.', 'GT', '0', '0', '0', './.', '0', '0', '0', '0', '0', '2', '0', '0']
['1', '1205', '.', 'A', '*,M', '.', '.', '.', 'GT', '0', '0', '0', './.', '0', '0', '0', '0', '2', '0', '0', '0']
['1', '1206', '.', 'A', '*,T,W', '.', '.', '.', 'GT', '0', '0', '0', './.', '2', '3', '2', '2', '2', '2', '2', '2']
['1', '1207', '.', 'C', '*,S', '.', '.', '.', 'GT', '0', '0', '0', './.', '0', '0', '0', '0', '0', '2', '0', '0']
['1', '1293', '.', 'C', '*,T', '.', '.', '.', 'GT', '0', '0', './.', './.', '0', '0', '0', '0', '0', '0', '2', '0']
['1', '1294', '.', 'T', '*,Y', '.', '.', '.', 'GT', '0', '0', './.', './.', '0', '0', '0', '0', '2', '0', '0', '0']
['1', '1295', '.', 'A', '*,C', '.', '.', '.', 'GT', '0', '0', './.', './.', '0', '0', '0', '0', '0', '0', '0', '2']
['1', '1296', '.', 'C', '*,G', '.', '.', '.', 'GT', '0', '0', './.', './.', '0', '0', '0', '0', '0', '2', '0', '0']
['1', '1333', '.', 'C', '*,S', '.', '.', '.', 'GT', './.', './.', './.', './.', './.', './.', './.', './.', '0', '0', '0', '2']
['1', '1334', '.', 'C', '*,Y', '.', '.', '.', 'GT', './.', './.', './.', './.', './.', './.', './.', './.', '0', '0', '0', '2']
['1', '1388', '.', 'T', '*,W', '.', '.', '.', 'GT', '0', '0', '0', '0', './.', './.', './.', '0', '0', '2', '0', '0']
['1', '1389', '.', 'A', 'M,*', '.', '.', '.', 'GT', '0', '0', '1', '0', './.', './.', './.', '0', '0', '0', '0', '0']
['1', '1390', '.', 'T', '*,G', '.', '.', '.', 'GT', '0', '0', '0', '0', './.', './.', './.', '2', '0', '0', '0', '0']
['1', '1391', '.', 'T', 'W,*', '.', '.', '.', 'GT', '0', '0', '1', '0', './.', './.', './.', '0', '0', '0', '0', '0']
['1', '1392', '.', 'G', '*,A', '.', '.', '.', 'GT', '0', '0', '0', '0', './.', './.', './.', '0', '2', '0', '0', '0']
['1', '1393', '.', 'G', 'S,*', '.', '.', '.', 'GT', '0', '0', '0', '1', './.', './.', './.', '0', '0', '0', '0', '0']
['1', '1411', '.', 'T', '*,C', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', '0', './.', './.', '0', '0', '0', '2']
['1', '1412', '.', 'T', 'W,*', '.', '.', '.', 'GT', '0', '0', '0', '0', '1', '0', './.', './.', '0', '0', '0', '0']
['1', '1471', '.', 'T', '*,A', '.', '.', '.', 'GT', './.', './.', './.', './.', '0', '0', '0', '0', '0', '0', '0', '2']
['1', '1472', '.', 'T', '*,K', '.', '.', '.', 'GT', './.', './.', './.', './.', '0', '0', '0', '0', '0', '0', '2', '0']
['1', '1473', '.', 'T', '*,A', '.', '.', '.', 'GT', './.', './.', './.', './.', '0', '0', '0', '0', '2', '2', '2', '2']
['1', '1474', '.', 'C', '*,M', '.', '.', '.', 'GT', './.', './.', './.', './.', '0', '0', '0', '0', '2', '0', '0', '0']
['1', '1475', '.', 'G', '*,S,C', '.', '.', '.', 'GT', './.', './.', './.', './.', '0', '0', '2', '3', '0', '0', '0', '0']
['1', '1686', '.', 'M', 'A,*', '.', '.', '.', 'GT', '0', '1', '1', '1', '1', './.', '1', '1', '1', '1', '1', '1']
['1', '1687', '.', 'T', 'G,*', '.', '.', '.', 'GT', '0', '0', '0', '0', '1', './.', '0', '0', '0', '0', '0', '0']
['1', '1688', '.', 'A', '*,C', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', './.', '0', '0', '0', '0', '2', '0']
['1', '1689', '.', 'A', '*,G', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', './.', '0', '0', '0', '0', '2', '0']
['1', '1690', '.', 'T', 'G,*', '.', '.', '.', 'GT', '0', '0', '0', '1', '0', './.', '0', '0', '0', '0', '0', '0']
['1', '1691', '.', 'T', '*,G', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', './.', '0', '0', '0', '0', '0', '2']
['1', '1692', '.', 'A', 'M,*', '.', '.', '.', 'GT', '0', '0', '0', '1', '0', './.', '0', '0', '0', '0', '0', '0']
['1', '1693', '.', 'G', 'A,*', '.', '.', '.', 'GT', '0', '0', '0', '1', '0', './.', '0', '0', '0', '0', '0', '0']
['1', '1962', '.', 'C', '*,G', '.', '.', '.', 'GT', '0', '0', '0', '0', './.', '0', '0', '0', '0', '0', '0', '2']
['1', '1963', '.', 'C', 'A,*', '.', '.', '.', 'GT', '0', '0', '0', '1', './.', '1', '1', '1', '1', '1', '1', '1']
['1', '1964', '.', 'C', '*,A', '.', '.', '.', 'GT', '0', '0', '0', '0', './.', '0', '0', '2', '0', '0', '0', '0']
['1', '1965', '.', 'G', '*,T', '.', '.', '.', 'GT', '0', '0', '0', '0', './.', '0', '0', '2', '0', '0', '0', '0']
['1', '2803', '.', 'T', '*,C', '.', '.', '.', 'GT', './.', './.', './.', '0', '0', '0', '0', '0', '0', '0', '0', '2']
['1', '2804', '.', 'G', '*,R', '.', '.', '.', 'GT', './.', './.', './.', '0', '0', '2', '0', '0', '0', '0', '0', '0']
['1', '3345', '.', 'T', '*,A', '.', '.', '.', 'GT', './.', './.', './.', './.', '0', '2', '2', './.', './.', './.', './.', './.']
['1', '4614', '.', 'A', '*,M', '.', '.', '.', 'GT', './.', './.', './.', './.', '0', '0', '2', './.', './.', './.', './.', './.']
['1', '4851', '.', 'G', '*,K', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', '0', '0', '0', './.', './.', '2', '0']
['1', '4852', '.', 'C', 'T,*', '.', '.', '.', 'GT', '0', '1', '1', '1', '1', '1', '1', '1', './.', './.', '1', '1']
['1', '4853', '.', 'T', 'Y,*', '.', '.', '.', 'GT', '0', '0', '0', '1', '0', '0', '0', '0', './.', './.', '0', '0']
['1', '4940', '.', 'G', '*,S', '.', '.', '.', 'GT', './.', './.', './.', './.', './.', './.', './.', './.', '0', '2', '0', '0']
['1', '4941', '.', 'T', '*,Y', '.', '.', '.', 'GT', './.', './.', './.', './.', './.', './.', './.', './.', '0', '2', '0', '0']
['1', '4942', '.', 'A', 'C,*', '.', '.', '.', 'GT', '0', '0', '0', '1', '1', '1', '1', '1', './.', './.', './.', '1']
['1', '4943', '.', 'A', 'W,*', '.', '.', '.', 'GT', '0', '0', '0', '0', '1', '1', '0', '0', './.', './.', './.', '0']
['1', '4944', '.', 'A', 'R,*', '.', '.', '.', 'GT', '0', '1', '0', '0', '0', '0', '0', '0', './.', './.', './.', '0']
['1', '4945', '.', 'G', 'K,*', '.', '.', '.', 'GT', '0', '1', '0', '0', '0', '0', '0', '0', './.', './.', './.', '0']
['1', '4946', '.', 'A', '*,T', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', '0', '0', '0', './.', './.', './.', '2']
['1', '4947', '.', 'G', '*,C', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', '0', '0', '0', './.', './.', './.', '2']
['1', '4948', '.', 'G', 'R,*', '.', '.', '.', 'GT', '0', '0', '0', '0', '1', '0', '0', '0', './.', './.', './.', '0']
['1', '4960', '.', 'T', 'G,*', '.', '.', '.', 'GT', '0', '0', '0', '1', './.', './.', './.', './.', './.', './.', './.', './.']
['1', '5536', '.', 'Y', '*,C', '.', '.', '.', 'GT', './.', './.', './.', './.', './.', './.', './.', './.', '0', '0', '2', './.']
['1', '6032', '.', 'T', '*,C', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', '0', '0', './.', '2', '2', '2', '0']
['1', '6033', '.', 'G', 'A,*', '.', '.', '.', 'GT', '0', '0', '1', '1', '1', '1', '1', './.', '1', '1', '1', '1']
['1', '6034', '.', 'A', 'M,*', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', '1', '0', './.', '1', '0', '0', '0']
['1', '6035', '.', 'A', '*,C', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', '0', '0', './.', '2', '2', '2', '0']
['1', '6036', '.', 'G', '*,R', '.', '.', '.', 'GT', '0', '0', '0', '0', '0', '0', '0', './.', '2', '0', '0', '0']
['1', '6507', '.', 'G', 'T,*', '.', '.', '.', 'GT', '0', '0', '1', '1', '1', '1', '1', '1', './.', '1', '1', '1']
['1', '6508', '.', 'A', 'G,*', '.', '.', '.', 'GT', '0', '1', '0', '0', '0', '0', '0', '0', './.', '0', '0', '0']
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