gkarthik

#!/bin/bash
#PBS -l walltime=400:00:00 -l mem=50gb -l nodes=1:ppn=16:ogtx -q gpu -o ~/logs/beast.txt -j oe

module load java
module load beagle

cd ~/analysis/

java -jar ~/bin/beast.jar -beagle_gpu 2018-08-18_Clade_CA_sampled_1_BV.xml
treeannotator -burnin 10000000 zika_cuba_dataset_jl.aligned.trees highest_posterior_tree.tree

gkarthik

2750000	-94946.5025 	-9837.1318  	-85109.3708 	11.7711     	16.9767     	36.8729     	13.6469     	15.6124     	8.86743     	5.08909E-309	1.69397E-2  	0.73 hours/million states
2760000	-94926.1453 	-9821.8959  	-85104.2494 	11.6039     	21.3436     	41.8054     	13.5893     	16.3518     	8.87767     	9.06455E-311	1.74763E-2  	0.73 hours/million states
2770000	-94947.0003 	-9833.4726  	-85113.5278 	11.7011     	22.0562     	33.8865     	13.5649     	13.8836     	8.90985     	1.43129E-312	2.19292E-2  	0.73 hours/million states
2780000	-94956.6478 	-9826.6588  	-85129.9890 	13.5314     	19.4467     	26.6005     	13.6477     	13.8686     	9.06803     	3.7914E-315 	1.93551E-2  	0.73 hours/million states
2790000	-94964.3947 	-9846.4740  	-85117.9207 	12.0128     	18.2168     	27.3915     	13.6542     	14.0305     	8.99086     	9.21056E-318	2.12541E-2  	0.73 hours/million states
2800000	-94894.6034 	-9795.5440  	-85099.0594 	11.6351     	17.2789     	36.4457     	13.7133     	13.8316     	8.94703     	9.4976E-319 	2

gkarthik

                  BEAST v1.8.4, 2002-2016
       Bayesian Evolutionary Analysis Sampling Trees
                 Designed and developed by
   Alexei J. Drummond, Andrew Rambaut and Marc A. Suchard
                              
               Department of Computer Science
                   University of Auckland
                  alexei@cs.auckland.ac.nz
                              
             Institute of Evolutionary Biology

gkarthik

import numpy as np
import matplotlib.pyplot as plt
import time

# Grid Structure = x * y * 2(Type, Number)
# Producer - 1
# Resistant - 2
# Sensitive - 3
# Killed - 4

gkarthik

Keybase proof

I hereby claim:

• I am gkarthik on github.
• I am gkarthik (https://keybase.io/gkarthik) on keybase.
• I have a public key whose fingerprint is 1501 7643 AA32 8623 391D 49AF A7B5 FD41 4BE6 439A

To claim this, I am signing this object:

gkarthik

Compilation started at Wed Mar 29 10:15:51

make -k
g++ -v -L ./include/ cluster_sequences.cpp -o cluster_sequences
Apple LLVM version 7.3.0 (clang-703.0.31)
Target: x86_64-apple-darwin15.6.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
 "/Library/Developer/CommandLineTools/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.11.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name cluster_sequences.cpp -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 264.3.102 -v -dwarf-column-info -resource-dir /Library/Developer/CommandLineTools/usr/bin/../lib/clang/7.3.0 -stdlib=libc++ -fdeprecated-macro -fdebug-compilation-dir /Users/karthik/Documents/code/pathogen-estimate -ferror-limit 19 -fmessage-length 131 -stack-protector 1 -fblocks -fobjc-runtime=macosx-10.11.0 -fencode-extended-block-signature -fcxx-excep

gkarthik

digraph {
	labelloc="t"
	label="PCA";
	node [shape=rect];
	rankdir = LR;

	
	a[label="Sample Data\nM0 = [(x1 ... x100)(y1....y100)]"];
	b[label="Centered Matrix\nM=[(x1-mean(x) ... x100-mean(x))(y1-mean(y)...y100-mean(y))]"];
	c[label="Sample covariance\nC = (MM')/(n-1)\nn=100"];

gkarthik

Sample	Percentage Coverage	Average Depth
ZF21-captest.trimmed.aligned.sorted.tsv	4.82	0.072
ZM3-captest.trimmed.aligned.sorted.tsv	12.30	0.22
Undetermined.trimmed.aligned.sorted.tsv	37.73	120.04
ZM1-captest.trimmed.aligned.sorted.tsv	3.47	5.80
Negctrl-captest.trimmed.aligned.sorted.tsv	4.82	0.09
ZF39-captest.trimmed.aligned.sorted.tsv	3.47	2.30

gkarthik

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please comment or extend with additional/faster/better solutions.

BWA mapping (using piping for minimal disk I/O)

gkarthik

Data

All the files can be accessed here: https://www.dropbox.com/sh/h2rt76o42qqnltx/AADOJveBz9p5D76nKPvMI9i6a?dl=0

Protocol can be found here: https://docs.google.com/document/d/1PilT4w5jHO-ROsE8TL5WBGa0wSCdTHAsNl1LIOYiTgk/

Methods