Contamination Detection in the Olive Genome: A Snakemake Workflow on AWS

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olive_genome
olive_genome
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This workflow includes analyses to find contamination in the domesticated olive genome. The results are presented in this preprint .

This workflow was run on a amazon aws instance (ubuntu/images/hvm-ssd/ubuntu-xenial-16.04-amd64-server-20171026.1 (ami-1c1d217c)). To run this workflow, you must first install and configure miniconda (or anaconda if you prefer).

Install miniconda 

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Run through the prompts.

Configure miniconda and create an environment 

conda config --add channels r
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda create -n snakemake python==3.6 snakemake=4.3.0 pysam=0.13 pandas=0.20.3 numpy=1.13.3 sourmash=2.0.0a2
conda activate snakemake

Then, run the workflow: 

snakemake --use-conda -k

Currently, the all rule dynamic("outputs/sylvestris/blast/tab/{contig_names_sylv}.tab") in the Snakefile is commented out. This means that the pipeline will only output Oe6 relevant files. To output sylvestris files, uncomment the rule, and comment the Oe6 rule.

Code Snippets

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    shell:'''
    wget -O {output.gz} http://denovo.cnag.cat/genomes/olive/download/Oe6/Oe6.scaffolds.fa.gz
    gunzip -c {output.gz} > {output.uncmp}
	'''
SnakeMake From line 10 of master/apulnucmer.snakefile 
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shell:'''
wget -O {output.sangz} ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/678/115/GCA_001678115.1_ASM167811v1/GCA_001678115.1_ASM167811v1_genomic.fna.gz 
gunzip -c {output.sangz} > {output.sanuncmp}
wget -O {output.ex150gz} ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/721/785/GCA_000721785.1_Aureobasidium_pullulans_var._pullulans_EXF-150_assembly_version_1.0/GCA_000721785.1_Aureobasidium_pullulans_var._pullulans_EXF-150_assembly_version_1.0_genomic.fna.gz
gunzip -c {output.ex150gz} > {output.ex150uncmp}
'''
SnakeMake From line 21 of master/apulnucmer.snakefile 
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shell:'''
nucmer --mum {input.Oe6} {input.san} -p outputs/aur-pul-nucmer/Oe6-APvarSan
'''
SnakeMake mummer2circos From line 34 of master/apulnucmer.snakefile 
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shell:'''
delta-filter -l 500 -q {input} > {output} 
'''
SnakeMake From line 42 of master/apulnucmer.snakefile 
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shell:'''
show-coords -c -l -L 500 -r -T {input} > {output}
'''
SnakeMake From line 50 of master/apulnucmer.snakefile 
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shell:'''
nucmer --mum {input.Oe6} {input.ex150} -p outputs/aur-pul-nucmer/Oe6-APvarEx
'''
SnakeMake mummer2circos From line 60 of master/apulnucmer.snakefile 
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shell:'''
delta-filter -l 500 -q {input} > {output}
'''
SnakeMake From line 68 of master/apulnucmer.snakefile 
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shell:'''
show-coords -c -l -L 500 -r -T {input} > {output}
'''
SnakeMake From line 76 of master/apulnucmer.snakefile 
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    shell:'''
    	wget -O {output.gz} http://denovo.cnag.cat/genomes/olive/download/Oe6/Oe6.scaffolds.fa.gz 
    	gunzip -c {output.gz} > {output.uncmp}
	'''
SnakeMake From line 13 of master/blast.snakefile 
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    shell:'''
		wget -O {output.gz} http://olivegenome.org/genome_datasets/Olea_europaea%3E1kb_scaffolds.gz
		gunzip -c {output.gz} > {output.uncmp}
    '''
SnakeMake From line 22 of master/blast.snakefile 
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shell:'''
	samtools faidx {input}
'''
SnakeMake SAMtools From line 31 of master/blast.snakefile 
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shell:'''
	samtools faidx {input}
'''
SnakeMake SAMtools From line 39 of master/blast.snakefile 
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run:
    fasta = pysam.Fastafile(filename = input.genome)
    f=open(input.contigs,'r')
    for line in f.readlines():
        # strip white space
        line = line.strip()
        # use pysam to grab the line of interest
        fasta_of_interest = fasta.fetch(line)
        with open(f"outputs/Oe6/suspicious_contigs/{line}.fa", "w") as text_file:
            # write content of fasta file with appropriate header and sequence
            text_file.write(f">{line}\n{fasta_of_interest}")
SnakeMake pysam From line 53 of master/blast.snakefile 
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run:
    fasta = pysam.Fastafile(filename = input.genome)
    f=open(input.contigs,'r')
    for line in f.readlines():
        # strip white space
        line = line.strip()
        # use pysam to grab the line of interest
        fasta_of_interest = fasta.fetch(line)
        with open(f"outputs/sylvestris/suspicious_contigs/{line}.fa", "w") as text_file:
            # write content of fasta file with appropriate header and sequence
            text_file.write(f">{line}\n{fasta_of_interest}")
SnakeMake pysam From line 71 of master/blast.snakefile 
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shell:'''
    cd inputs/blast_db
	wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt.*.tar.gz'
	cat nt.*.tar.gz | tar -zxvi -f - -C .
'''
SnakeMake From line 87 of master/blast.snakefile 
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shell:'''
	blastn -query {input.contig} -db inputs/blast_db/nt -outfmt 11 -out {output}
'''
SnakeMake BLAST From line 99 of master/blast.snakefile 
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shell:'''
	blastn -query {input.contig} -db inputs/blast_db/nt -outfmt 11 -out {output}
'''
SnakeMake BLAST From line 109 of master/blast.snakefile 
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shell:'''
	blast_formatter -archive {input} -outfmt 6 -out {output}
'''
SnakeMake From line 117 of master/blast.snakefile 
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shell:'''
	blast_formatter -archive {input} -outfmt 6 -out {output}
'''
SnakeMake From line 125 of master/blast.snakefile 
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    shell:'''
	wget -O {output.gz} http://olivegenome.org/genome_datasets/Olea_europaea_all_scaffolds.fa.gz 
	gunzip -c {output.gz} > {output.uncmp}
	'''
SnakeMake From line 8 of master/busco.snakefile 
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    shell:'''
    wget -O {output.tgz} http://busco.ezlab.org/datasets/embryophyta_odb9.tar.gz
	mkdir -p {output.db}
    tar -xf {output.tgz} --strip-components=1 -C {output.db}
    '''
SnakeMake From line 17 of master/busco.snakefile 
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    shell:'''
	run_busco -i {input.genome} -o wild_olive_busco -l {input.busco_db} -m geno
        mv run_wild_olive_busco {output}
    '''
SnakeMake From line 28 of master/busco.snakefile 
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    shell:'''
    wget -O {output.gz} http://denovo.cnag.cat/genomes/olive/download/Oe6/Oe6.scaffolds.fa.gz 
    gunzip -c {output.gz} > {output.uncmp}
	'''
SnakeMake From line 8 of master/olivenucmer.snakefile 
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    shell:'''
	wget -O {output.gz} http://olivegenome.org/genome_datasets/Olea_europaea_chromosome+unchromosome.gz 
	gunzip -c {output.gz} > {output.uncmp}
	'''
SnakeMake From line 17 of master/olivenucmer.snakefile 
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shell:'''
nucmer --mum {input.sylv} {input.Oe6} -p outputs/olive_genomes_nucmer/sylvester_santander_nucmer
'''
SnakeMake mummer2circos From line 28 of master/olivenucmer.snakefile 
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shell:'''
delta-filter -l 500 -q {input} > {output}
'''
SnakeMake From line 36 of master/olivenucmer.snakefile 
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shell:'''
show-coords -c -l -L 500 -r -T {input} > {output}
'''
SnakeMake From line 44 of master/olivenucmer.snakefile 
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    shell:'''
    wget -O {output} http://denovo.cnag.cat/genomes/olive/download/Oe6/OE6A.pep.fa 
	'''
SnakeMake From line 6 of master/orthofinder.snakefile 
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    shell:'''
	wget -O {output.gz} http://olivegenome.org/genome_datasets/Olea_europaea.gene.pep.final.chr_and_chrUn_noTE.gz 
	gunzip -c {output.gz} > {output.uncmp}
	'''
SnakeMake From line 14 of master/orthofinder.snakefile 
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    shell:'''
	orthofinder -f inputs/peptides -og
	cp -a inputs/peptides/Results*/. {output}
	'''
SnakeMake OrthoFinder From line 32 of master/orthofinder.snakefile 
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shell:'''
	wget -O {output} http://denovo.cnag.cat/genomes/olive/download/Oe6/Oe6.scaffolds.fa.gz
'''
SnakeMake From line 8 of master/sourmashlca.snakefile 
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    shell:'''
		wget -O {output} http://olivegenome.org/genome_datasets/Olea_europaea%3E1kb_scaffolds.gz
	'''
SnakeMake From line 14 of master/sourmashlca.snakefile 
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shell:'''
# compute tetranucleotide frequency of scaffolds
	sourmash compute -k 31 --scaled 10000 -o {output} {input}
'''
SnakeMake From line 22 of master/sourmashlca.snakefile 
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shell:'''
# compute tetranucleotide frequency of scaffolds
	sourmash compute -k 31 --scaled 10000 -o {output} {input}
'''
SnakeMake From line 31 of master/sourmashlca.snakefile 
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shell:'''
	wget -O inputs/genbank_lca/genbank-k31.lca.json.gz https://osf.io/zskb9/download
'''
SnakeMake From line 38 of master/sourmashlca.snakefile 
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shell:'''
	sourmash lca classify --db {input.genbank} --query {input.sig} -o {output}
'''
SnakeMake From line 48 of master/sourmashlca.snakefile 
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shell:'''
sourmash lca classify --db {input.genbank} --query {input.sig} -o {output}
'''
SnakeMake From line 58 of master/sourmashlca.snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/taylorreiter/olive_genome
Name: olive_genome
Version: 1
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Copyright: Public Domain
License: BSD 3-Clause "New" or "Revised" License
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