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#!/bin/bash | ||
#SBATCH --job-name=raxml | ||
#SBATCH -N 1 | ||
#SBATCH -n 1 | ||
#SBATCH -c 16 | ||
#SBATCH --partition=amd | ||
#SBATCH --mail-type=END | ||
#SBATCH --mem=20G | ||
#SBATCH --mail-user=yutian.feng@uconn.edu | ||
#SBATCH -o racks_%j.out | ||
#SBATCH -e racks_%j.err | ||
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module load RAxML/8.2.11 | ||
raxmlHPC f i t extein.te z inteinaa.align.ufboot m GTRCAT n T4 | ||
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#!/bin/bash | ||
#SBATCH --job-name=tblastn | ||
#SBATCH -N 1 | ||
#SBATCH -n 1 | ||
#SBATCH -c 6 | ||
#SBATCH --partition=amd | ||
#SBATCH --mail-type=END | ||
#SBATCH --mem=250G | ||
#SBATCH --mail-user=yutian.feng@uconn.edu | ||
#SBATCH -o tblastn_%j.out | ||
#SBATCH -e tblastn_%j.err | ||
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module load iqtree/1.5.5 | ||
iqtree-omp -s inteinaa.align -st AA -m LG+F+I+G4 -n 0 -z exteinaa.ufb -zb 1000 -au -nt AUTO | ||
iqtree-omp -s exteinaa.align -st AA -m LG+F+R5 -n 0 -z inteinaa.ufb -zb 1000 -au -nt AUTO |
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#!/bin/bash | ||
#$ -N ass | ||
#$ -M yutian.feng@uconn.edu | ||
#$ -q all.q | ||
#$ -m ea | ||
#$ -S /bin/bash | ||
#$ -cwd | ||
#$ -pe smp 16 | ||
#$ -o ass_$JOB_ID.out | ||
#$ -e ass_$JOB_ID.err | ||
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cd /home/yuf17006/metagenomes | ||
module load SPAdes/3.10.0 | ||
spades.py --meta --only-asembler --pe<1>-1 ERR1739731_1.fastq --pe<1>-2 ERR1739731_2.fastq -o test1 | ||
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#!/usr/bin/perl -w | ||
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use strict; | ||
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my $infasta=$ARGV[0]; | ||
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open FH1 , "$infasta" or die "$!"; | ||
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my @sequence =""; | ||
my $first = ""; | ||
my $second =""; | ||
my $begin=""; | ||
my $end=""; | ||
my $front = ""; | ||
my $back = ""; | ||
my $final = ""; | ||
while(<FH1>){ | ||
chomp; | ||
@sequence = split /\t/, $_; | ||
$first = $sequence[6]; | ||
$second = $sequence[7]; | ||
if ($first > $second) { | ||
$begin = $second; | ||
$end = $first; | ||
} | ||
else{ | ||
$begin = $first; | ||
$end = $second; | ||
} | ||
my $frontflank = int($begin)-1000; | ||
my $backflank = int($end+1000); | ||
my $seqname = $sequence[0]; | ||
open FH2, "$seqname".".seqfile"; | ||
my $worthless =""; | ||
my $cds= ""; | ||
while(<FH2>){ | ||
chomp; | ||
if(/^\>(.*)/){ | ||
$worthless = $worthless . $_; | ||
} | ||
else{ | ||
$cds = $cds . $_; | ||
} | ||
} | ||
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my @readin = split //, $cds; | ||
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while ($frontflank < $backflank){ | ||
$front = $front . $readin[$frontflank]; | ||
$frontflank += 1; | ||
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} | ||
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$final = $front ; | ||
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print ">".$sequence[0].".seqfile2\n".$final."\n"; | ||
@sequence =""; | ||
$front =""; | ||
$final =""; | ||
$back =""; | ||
$first = ""; | ||
$second =""; | ||
$begin=""; | ||
$end=""; | ||
} |
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#!/usr/bin/perl -w | ||
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use strict; | ||
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my $infasta=$ARGV[0]; | ||
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open FH1 , "$infasta" or die "$!"; | ||
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my @sequence =""; | ||
my $first = ""; | ||
my $second =""; | ||
my $begin=""; | ||
my $end=""; | ||
my $front = ""; | ||
my $back = ""; | ||
my $final = ""; | ||
while(<FH1>){ | ||
chomp; | ||
@sequence = split /\t/, $_; | ||
$first = $sequence[6]; | ||
$second = $sequence[7]; | ||
if ($first > $second) { | ||
$begin = $second; | ||
$end = $first; | ||
} | ||
else{ | ||
$begin = $first; | ||
$end = $second; | ||
} | ||
my $seqname = $sequence[0]; | ||
open FH2, "$seqname".".seqfile2"; | ||
my $worthless =""; | ||
my $cds= ""; | ||
while(<FH2>){ | ||
chomp; | ||
if(/^\>(.*)/){ | ||
$worthless = $worthless . $_; | ||
} | ||
else{ | ||
$cds = $cds . $_; | ||
} | ||
} | ||
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my @readin = split //, $cds; | ||
my $i =0; | ||
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while ($i < $begin){ | ||
$front = $front . $readin[$i]; | ||
$i += 1; | ||
} | ||
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while ($end < $#readin){ | ||
$back = $back . $readin[$end]; | ||
$end += 1; | ||
} | ||
$final = $front . $back; | ||
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print ">".$sequence[0].".ext\n".$final."\n"; | ||
@sequence =""; | ||
$front =""; | ||
$final =""; | ||
$back =""; | ||
$first = ""; | ||
$second =""; | ||
$begin=""; | ||
$end=""; | ||
} |
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#!/bin/bash | ||
#SBATCH --job-name=raxml | ||
#SBATCH -N 1 | ||
#SBATCH -n 1 | ||
#SBATCH -c 16 | ||
#SBATCH --partition=amd | ||
#SBATCH --mail-type=END | ||
#SBATCH --mem=20G | ||
#SBATCH --mail-user=yutian.feng@uconn.edu | ||
#SBATCH -o racks_%j.out | ||
#SBATCH -e racks_%j.err | ||
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module load RAxML/8.2.11 | ||
raxmlHPC -f i -t extein.te -z inteinaa.align.ufboot -m GTRCAT -n T4 |
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#!/bin/bash | ||
#SBATCH --job-name=reroot | ||
#SBATCH -N 1 | ||
#SBATCH -n 1 | ||
#SBATCH -c 6 | ||
#SBATCH --partition=amd | ||
#SBATCH --mail-type=END | ||
#SBATCH --mem=50G | ||
#SBATCH --mail-user=yutian.feng@uconn.edu | ||
#SBATCH -o reroot_%j.out | ||
#SBATCH -e reroot_%j.err | ||
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module load iqtree/1.5.5 | ||
iqtree-omp -s cdsall7.align -nt AUTO -bb 1000 -st AA |
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#!/bin/bash | ||
#SBATCH --job-name=kraken | ||
#SBATCH -N 1 | ||
#SBATCH -n 1 | ||
#SBATCH -c 24 | ||
#SBATCH --partition=himem4 | ||
#SBATCH --mail-type=END | ||
#SBATCH --mem=250G | ||
#SBATCH --mail-user=yutian.feng@uconn.edu | ||
#SBATCH -o kraken_%j.out | ||
#SBATCH -e kraken_%j.err | ||
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module load kraken/1.0 | ||
kraken -d /isg/shared/databases/kraken/standard contigs.fasta --threads 24 |
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#!/bin/bash | ||
#SBATCH --job-name=metabat | ||
#SBATCH -N 1 | ||
#SBATCH -n 1 | ||
#SBATCH -c 24 | ||
#SBATCH --partition=himem4 | ||
#SBATCH --mail-type=END | ||
#SBATCH --mem=250G | ||
#SBATCH --mail-user=yutian.feng@uconn.edu | ||
#SBATCH -o metabat_%j.out | ||
#SBATCH -e metabat_%j.err | ||
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module load metabat/2.12.1 | ||
metabat -i contigs.fasta.gz -o binout |
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#!/bin/bash | ||
#SBATCH --job-name=metabat | ||
#SBATCH -N 1 | ||
#SBATCH -n 1 | ||
#SBATCH -c 24 | ||
#SBATCH --partition=himem4 | ||
#SBATCH --mail-type=END | ||
#SBATCH --mem=250G | ||
#SBATCH --mail-user=yutian.feng@uconn.edu | ||
#SBATCH -o metabat_%j.out | ||
#SBATCH -e metabat_%j.err | ||
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module load metabat/2.12.1 | ||
metabat -i contigs.fasta.gz -o binout |
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#!/bin/bash | ||
#SBATCH --job-name=assing | ||
#SBATCH -N 1 | ||
#SBATCH -n 1 | ||
#SBATCH -c 16 | ||
#SBATCH --partition=himem4 | ||
#SBATCH --mail-type=END | ||
#SBATCH --mem=500G | ||
#SBATCH --mail-user=yutian.feng@uconn.edu | ||
#SBATCH -o assing_%j.out | ||
#SBATCH -e assing_%j.err | ||
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module load SPAdes/3.11.1 | ||
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spades.py --pe1-1 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739732_1.trim.fq --pe1-2 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739732_2.trim.fq -o assembly2 | ||
spades.py --pe1-1 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739731_1.trim.fq --pe1-2 /UCHC/LABS/Gogarten/metagenomes/meyghan/ERR1739731_2.trim.fq -o assembly3 |
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