peterdfields

brew install --HEAD beagle --with-cuda -v
==> Checking out http://beagle-lib.googlecode.com/svn/trunk/
svn up --force /Library/Caches/Homebrew/beagle--svn-HEAD
At revision 1092.
svn export --force /Library/Caches/Homebrew/beagle--svn-HEAD /private/tmp/beagle-mDzX
Export complete.
==> Patching
/usr/bin/patch -f -p1 -i 000-homebrew.diff
patching file configure.ac
==> ./autogen.sh

peterdfields

mkdir -p -- /home/peter/.linuxbrew/Cellar/r/3.0.2/lib64/R
make[1]: Entering directory `/tmp/r-6k7o/R-3.0.2/m4'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/tmp/r-6k7o/R-3.0.2/m4'
make[1]: Entering directory `/tmp/r-6k7o/R-3.0.2/tools'
make[1]: Nothing to be done for `install'.
make[1]: Leaving directory `/tmp/r-6k7o/R-3.0.2/tools'
make[1]: Entering directory `/tmp/r-6k7o/R-3.0.2/doc'
installing doc ...
mkdir -p -- /home/peter/.linuxbrew/Cellar/r/3.0.2/lib64/R/doc

peterdfields

@HD	VN:1.4	SO:coordinate
@SQ	SN:scaffold_0	LN:533418
@SQ	SN:scaffold_1	LN:488922
@SQ	SN:scaffold_2	LN:473555
@SQ	SN:scaffold_3	LN:451417
@SQ	SN:scaffold_4	LN:431695
@SQ	SN:scaffold_5	LN:424084
@SQ	SN:scaffold_6	LN:432731
@SQ	SN:scaffold_7	LN:423419
@SQ	SN:scaffold_8	LN:418380

peterdfields

@HD	VN:1.4	SO:coordinate
@SQ	SN:scaffold_0	LN:533418
@SQ	SN:scaffold_1	LN:488922
@SQ	SN:scaffold_2	LN:473555
@SQ	SN:scaffold_3	LN:451417
@SQ	SN:scaffold_4	LN:431695
@SQ	SN:scaffold_5	LN:424084
@SQ	SN:scaffold_6	LN:432731
@SQ	SN:scaffold_7	LN:423419
@SQ	SN:scaffold_8	LN:418380

peterdfields

@HD	VN:1.4	SO:coordinate
@SQ	SN:scaffold_0	LN:533418
@SQ	SN:scaffold_1	LN:488922
@SQ	SN:scaffold_2	LN:473555
@SQ	SN:scaffold_3	LN:451417
@SQ	SN:scaffold_4	LN:431695
@SQ	SN:scaffold_5	LN:424084
@SQ	SN:scaffold_6	LN:432731
@SQ	SN:scaffold_7	LN:423419
@SQ	SN:scaffold_8	LN:418380

peterdfields

[INFO]Setup logging from file "None".
[INFO]# of tasks in complete graph: 1
[INFO]tick: 1, #updatedTasks: 0, sleep_time=0.000000
[INFO] Skipping already done task: task://localhost/track_reads
[INFO]_refreshTargets() finished with no thread running and no new job to submit
[INFO]# of tasks in complete graph: 583
[INFO]tick: 1, #updatedTasks: 0, sleep_time=0.000000
[INFO] Skipping already done task: task://localhost/aln_000080F
[INFO] Skipping already done task: task://localhost/p_000080F
[INFO] Skipping already done task: task://localhost/aln_000152F

peterdfields

import gzip
import csv
import argparse
import sys

parser = argparse.ArgumentParser(description="script to convert an all sites vcf to sweepfinder format. FASTA description will be the sample name in the VCF header.Only does one chromosome/region at a time.")
parser.add_argument("-v", "--vcf", action="store", required=True, help="Input VCF file. Should be a multisample vcf, though it should theoretically work with a single sample.")
parser.add_argument("-o", "--out", action="store", required=True, help="Output filename")
parser.add_argument("-c", "--chromosome", action="store", required=True, help="Chromosome to output. Should be something in the first column of the vcf.")
parser.add_argument("-g", "--gzip", action="store_true", required=False, help="Set if the VCF is gzipped.")

peterdfields

import gzip
import csv
import argparse
import sys

parser = argparse.ArgumentParser(description="script to convert an all sites vcf to FASTA format. FASTA description will be the sample name in the VCF header.Only does one chromosome/region at a time.")
parser.add_argument("-v", "--vcf", action="store", required=True, help="Input VCF file. Should be a multisample vcf, though it should theoretically work with a single sample.")
parser.add_argument("-o", "--out", action="store", required=True, help="Output filename")
parser.add_argument("-c", "--chromosome", action="store", required=True, help="Chromosome to output. Should be something in the first column of the vcf.")
parser.add_argument("-g", "--gzip", action="store_true", required=False, help="Set if the VCF is gzipped.")

peterdfields

##GTR lset applyto=() nst=6 # GTR lset applyto=() nst=6 rates=propinv # GTR + I lset applyto=() nst=6 rates=gamma # GTR + gamma lset applyto=() nst=6 rates=invgamma # GTR + I + gamma

##SYM

lset applyto=() nst=6                           # SYM

prset applyto=() statefreqpr=fixed(equal)

peterdfields

---- Running command
---- ./polyDFE -d input/Control_uSFS_pdfe.txt -v 1 -b -t -e -w 
---- Performing inference on input/Control_uSFS_pdfe.txt using model C

---- Running basin hopping with default values
---- Data does not contain divergence counts. Using option -w.
---- No mutation variability. Using Poisson likelihood.

---- Starting a maximum of 500 basin hopping iterations