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Snakefile
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# Ideally, format your hostcoes as 'species'_'accession'_'uniquenr/library/strain/treatment' for later automatic processing.
HOSTCODES= ['Azrub_IRRI_479','Azfil_lab_250', 'Azfil_lab_500', 'Azfil_lab_800', 'Azfil_minuscyano_170', 'Azfil_minuscyano_350', 'Azfil_wild_galgw_E_1', 'Azfil_wild_galgw_E_2', 'Azfil_wild_galgw_E_3', 'Azfil_wild_galgw_P_2', 'Azfil_wild_galgw_P_3', 'Azfil_wild_galgw_P_4', 'Azmex_IRRI_486', 'Azmic_IRRI_456', 'Aznil_IRRI_479', 'Azspnov_IRRI1_472', 'Azspnov_IRRI2_489']
DIRECTIONS=["1","2"]
# refined is a manual subset of the final libraries/assemblies chosen for final analysis
REFINED = ['Azrub_IRRI_479', 'Azfil_lab', 'Azfil_minuscyano', 'Azfil_wild', 'Azmex_IRRI_486', 'Azmic_IRRI_456', 'Aznil_IRRI_479', 'Azspnov_IRRI1_472', 'Azspnov_IRRI2_489']
# Assuming that host codes are formated as 'species'_'accession'_'uniquenr/library/strain/treatment' the following line of code
# autmatically creates an array of host accession combinations for cross-assembly of different strains,sequencing libraries, treatments.
# Likewise, the code below creates a list of species which have multiple sequencing libraries.
def get_species_cross_assembly():
return_species=set([])
for i in set([i.split('_',3)[0] for i in HOSTCODES]):
species_sub=list(filter(lambda x:i in x, HOSTCODES))
if len(species_sub) >= 2 :
return_species.add(i)
return(list(return_species))
def get_hosts_cross_assembly():
return_hosts=set([])
for i in set([i.split('_',3)[0] + '_' + i.split('_',3)[1] for i in HOSTCODES]):
host_sub=list(filter(lambda x:i in x, HOSTCODES))
if len(host_sub) >= 2 :
return_hosts.add(i)
return(list(return_hosts))
def get_single_hosts():
return_hosts=set([])
for i in HOSTCODES:
species = i.split('_',3)[0] + '_' + i.split('_',3)[1]
host_sub = list(filter(lambda x:species in x, HOSTCODES))
if len(host_sub) == 1 :
return_hosts.add(i)
return(list(return_hosts))
SPECIES=get_species_cross_assembly()
HOSTS=get_hosts_cross_assembly()
SINGLEHOSTS=get_single_hosts()
ASSEMBLYTYPES=['singles_doublefiltered','singles_hostfiltered'] # ,'hybrid_doublefiltered'] #,'species_doublefiltered']
# Ideally these should only contain letter, numbers and underscores. Exceptionally, these can contain points but they will be replaced by underscores for anvi'o
BINNINGSIGNALS=['dijkhuizen2018.E.1', 'dijkhuizen2018.E.2', 'dijkhuizen2018.E.3', 'dijkhuizen2018.P.2', 'dijkhuizen2018.P.3', 'dijkhuizen2018.P.4','ran2010.nostoc.SRR066216','ran2010.nostoc.SRR066217','ran2010.nostoc.SRR3923641','ran2010.nostoc.SRR3923645','ran2010.nostoc.SRR3923646']
ASSEMBLYFILES=['contigs','scaffolds']
## 'All'-rules
rule all_assemblies_and_annotations:
input:
"analyses/assembly_stats_and_taxonomy.tab",
expand("data/bins_{assemblytype}/{hostcode}.BAT.names.txt",assemblytype=ASSEMBLYTYPES,hostcode=HOSTCODES),
expand("data/bins_{assemblytype}_checkm/{hostcode}/{hostcode}.checkm_out",assemblytype=ASSEMBLYTYPES,hostcode=HOSTCODES),
expand("data/assembly_{assemblytype}_anvio/{hostcode}/{hostcode}_contigs_db_run_ncbi_cogs.done",assemblytype='singles_doublefiltered',hostcode=HOSTCODES),
expand("data/assembly_{assemblytype}_binningsignals_anvio/MERGED_{hostcode}/CAT_taxonomy_imported.done",assemblytype='singles_doublefiltered',hostcode=HOSTCODES),
expand("data/assembly_{assemblytype}_binningsignals_anvio/MERGED_{hostcode}/PROFILE_db_imported-metabat2.done",assemblytype='singles_doublefiltered',hostcode=HOSTCODES),
"analyses/assembly-hybrid_stats_and_taxonomy.tab",
expand("data/bins_{assemblytype}/{hostcode}.BAT.names.txt",assemblytype='hybrid_doublefiltered',hostcode=HOSTS),
expand("data/bins_{assemblytype}_checkm/{hostcode}/{hostcode}.checkm_out",assemblytype='hybrid_doublefiltered',hostcode=HOSTS),
expand("data/assembly_{assemblytype}_anvio/{hostcode}/{hostcode}_contigs_db_run_ncbi_cogs.done",assemblytype='hybrid_doublefiltered',hostcode=HOSTS),
expand("data/assembly_{assemblytype}_binningsignals_anvio/MERGED_{hostcode}/CAT_taxonomy_imported.done",assemblytype='hybrid_doublefiltered',hostcode=HOSTS),
expand("data/assembly_{assemblytype}_binningsignals_anvio/MERGED_{hostcode}/PROFILE_db_imported-metabat2.done",assemblytype='hybrid_doublefiltered',hostcode=HOSTS)
rule all_exported_bins:
input:
expand("data/curated_bins/{{collection}}/{hostcode}",hostcode=HOSTS),
expand("data/curated_bins/{{collection}}/{hostcode}",hostcode=SINGLEHOSTS)
output:
touch("data/curated_bins/{collection}.exported")
rule all_exported_bins_refined_checkm_BAT:
input:
expand("data/curated_bins/{collection}/{hostcode}/{hostcode}.checkm_out.txt", collection='refined', hostcode=REFINED),
expand("data/curated_bins/{collection}/{hostcode}/{hostcode}.BAT.names.txt" , collection='refined', hostcode=REFINED)
rule trim:
input:
expand("data/sequencing_genomic_trimmed/{hostcode}_R{PE}.fastq.gz",hostcode=HOSTCODES,PE=DIRECTIONS)
## Read QC stuff and rules for a data flow figure
rule fastqc_raw_data:
input:
"data/sequencing_genomic/{hostcode}_R{PE}.fastq.gz"
output:
directory("analyses/analyses_reads/{hostcode}_{PE}")
shell:
"mkdir {output} 2> /dev/null && fastqc -o {output} {input}"
rule fastqc_trimmed_data:
input:
"data/sequencing_genomic_trimmed/{hostcode}_{PE}.fastq.gz"
output:
directory("analyses/analyses_reads/{hostcode}_{PE}")
shell:
"mkdir {output} 2> /dev/null && fastqc -o {output} {input}"
rule fastqc_filtered_data:
input:
"data/sequencing_genomic_trimmed_filtered_corrected/{hostcode}/corrected/{hostcode}.{PE}.fastq.00.0_0.cor.fastq.gz"
output:
directory("analyses/analyses_reads_trimmed_filtered/{hostcode}_{PE}")
shell:
"mkdir {output} 2> /dev/null && fastqc -o {output} {input}"
rule fastqc_doublefiltered_data:
input:
"data/sequencing_doublefiltered/{hostcode}/{hostcode}.{PE}.fastq.gz"
output:
directory("analyses/analyses_reads_doublefiltered/{hostcode}_{PE}")
shell:
"mkdir {output} 2> /dev/null && fastqc -o {output} {input}"
rule collect_reads_stats:
input:
expand("analyses/analyses_reads/{hostcode}_{PE}" ,hostcode=HOSTCODES,PE=DIRECTIONS),
expand("analyses/analyses_reads_trimmed/{hostcode}_{PE}" ,hostcode=HOSTCODES,PE=DIRECTIONS),
expand("analyses/analyses_reads_trimmed_filtered/{hostcode}_{PE}" ,hostcode=HOSTCODES,PE=DIRECTIONS),
expand("analyses/analyses_reads_doublefiltered/{hostcode}_{PE}" ,hostcode=HOSTCODES,PE=DIRECTIONS)
# expand("data/assembly_{assemblytype}/{hostcode}/{assemblyfile}.fasta",assemblytype=ASSEMBLYTYPES,hostcode=HOSTCODES,assemblyfile='contigs')
output:
"analyses/reads_stats.tab"
shell:
"bash ./scripts/collect_reads_stats.bash > {output}"
## reference rules
rule download_azolla_genome:
output:
"references/host_genome/host_genome.fasta"
shell:
"wget ftp://ftp.fernbase.org/Azolla_filiculoides/Azolla_asm_v1.1/Azolla_filiculoides.genome_v1.2.fasta -O {output}"
rule download_azolla_proteins:
output:
"references/host_genome/host_proteins.fasta"
shell:
"wget ftp://ftp.fernbase.org/Azolla_filiculoides/Azolla_asm_v1.1/Azolla_filiculoides.protein.highconfidence_v1.1.fasta -O {output}"
rule CAT_download:
output:
# db=temp("references/CAT_prepare_20190108/2019-01-08_CAT_database"),
tf=temp("references/CAT_prepare_20190108/2019-01-08_taxonomy"),
nr=temp("references/CAT_prepare_20190108/2019-01-08_CAT_database/2019-01-08.nr.gz")
shell:
"cd ./references && wget -qO - http://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20190108.tar.gz | tar -xz"
rule CAT_customise:
input:
db="references/CAT_prepare_20190108/2019-01-08_CAT_database/2019-01-08.nr.gz",
tf="references/CAT_prepare_20190108/2019-01-08_taxonomy",
custom_proteins="references/host_genome/host_proteins.fasta"
output:
nr="references/CAT_customised_20190108/CAT_database_customised/2019-1-08.nr.gz",
db=directory("references/CAT_customised_20190108/CAT_database_customised"),
tf=directory("references/CAT_customised_20190108/taxonomy_customised"),
tf_id="references/CAT_customised_20190108/taxonomy_customised/2019-01-08.prot.accession2taxid.gz"
shell:
"""
cp {input.db} {output.nr}
cp -r {input.tf}/* {output.tf}
pigz -c {input.custom_proteins} >> {output.nr}
grep '>' {input.custom_proteins} | tr -d '>' | awk -v OFS='\t' '{{print $0, $0, 84609, 0}}' | pigz -c >> {output.tf_id}
"""
rule CAT_build:
input:
db="references/CAT_customised_20190108/CAT_database_customised",
tf="references/CAT_customised_20190108/taxonomy_customised"
output:
"references/CAT_customised_20190108/CAT_database_customised/2019-03-27.nr.dmnd"
log:
stdout="logs/CAT_build_nr+host.stdout",
stderr="logs/CAT_build_nr+host.stderr"
threads: 100
shell:
"CAT prepare --existing -d {input.db} -t {input.tf} -n {threads} > {log.stdout} 2> {log.stderr}"
rule CAT_prepare_ORFS_host:
input:
"references/host_genome/host_genome.fasta"
output:
p="references/host_genome/host.predicted_proteins.faa",
g="references/host_genome/host.predicted_proteins.gff",
params:
"-p meta -g 11 -q -f gff"
threads: 1
log:
stdout="logs/CAT_host_prodigal.stdout",
stderr="logs/CAT_host_prodigal.stderr"
shell:
"prodigal -i {input} -a {output.p} -o {output.g} {params} 2> {log.stderr} > {log.stdout}"
rule CAT_classify_host:
input:
prot="references/host_genome/host.predicted_proteins.faa",
contigs="references/host_genome/host_genome.fasta",
dmnd="references/CAT_customised_20190108/CAT_database_customised/2019-03-27.nr.dmnd",
db="references/CAT_customised_20190108/CAT_database_customised",
tf="references/CAT_customised_20190108/taxonomy_customised"
params:
prefix="references/host_genome/CAT/host",
options="-r 5"
output:
i="references/host_genome/CAT/host.contig2classification.txt"
threads: 100
shadow: 'shallow'
log:
stdout="logs/CAT_classify_host.stdout",
stderr="logs/CAT_classify_host.stderr"
shell:
"CAT contigs {params.options} -p {input.prot} -c {input.contigs} -d {input.db} -t {input.tf} --out_prefix {params.prefix} -n {threads} 2> {log.stderr} > {log.stdout}"
# shall I remove host.alignment.diamond, it's huge and does not serve a purpose further on.
rule CAT_add_names:
input:
i="references/host_genome/CAT/host.contig2classification.txt",
tf="references/CAT_customised_20190108/taxonomy_customised"
output:
"references/host_genome/contig_taxonomy.tab"
log:
stdout="logs/CAT_addnames_host.stdout",
stderr="logs/CAT_addnames_host.stderr"
params: "--only_official"
threads: 1
shell:
"CAT add_names {params} -i {input.i} -t {input.tf} -o {output} > {log.stdout} 2> {log.stderr}"
rule CAT_filter_contignames:
input:
"references/host_genome/contig_taxonomy.tab"
output:
"references/host_genome/contig_filterlist.txt"
threads: 1
log:
"logs/CAT_contigfilterlist.stderr"
shell:
"cat {input} | grep -v '#' | grep -v Bacteria | cut -f 1 > {output} 2> {log}"
rule CAT_get_bacterial_contignames:
input:
"references/host_genome/contig_taxonomy.tab"
output:
"references/host_genome/bacterial_contigs.txt"
threads: 1
log:
"logs/CAT_contigfilterlist.stderr"
shell:
"cat {input} | grep -v '#' | grep Bacteria | cut -f 1 > {output} 2> {log}"
rule create_host_bacterialcontigs_fasta:
input:
n="references/host_genome/bacterial_contigs.txt",
f="references/host_genome/host_genome.fasta"
output:
expand("references/host_genome/{host}_host-genome_bacterial_contigs.fasta",host='Azfil_lab')
threads: 1
log:
stdout="logs/CAT_create_host_bacterial_contigs.stdout",
stderr="logs/CAT_create_host_bacterial_contigs.stderr"
shell:
"samtools faidx {input.f} -o {output} -r {input.n} > {log.stdout} 2> {log.stderr}"
rule create_host_filter_fasta:
input:
n="references/host_genome/contig_filterlist.txt",
f="references/host_genome/host_genome.fasta"
output:
"references/host_genome/host_filter.fasta"
threads: 1
log:
stdout="logs/CAT_createhostfilter.stdout",
stderr="logs/CAT_createhostfilter.stderr"
shell:
"samtools faidx {input.f} -o {output} -r {input.n} > {log.stdout} 2> {log.stderr}"
rule create_host_filter_bt2_index:
input:
"references/host_genome/host_filter.fasta"
params:
"references/host_genome/host_filter_bt2index/host_filter"
output:
expand("references/host_genome/host_filter_bt2index/host_filter.{i}.bt2",i=range(1,4)),
expand("references/host_genome/host_filter_bt2index/host_filter.rev.{i}.bt2",i=range(1,2))
threads: 100
log:
stdout="logs/CAT_createhostfilterbt2index.stdout",
stderr="logs/CAT_createhostfilterbt2index.stderr"
shell:
"bowtie2-build --threads {threads} {input} {params} > {log.stdout} 2> {log.stderr}"
## data processing rules
rule trimmomatic_genomic_sequencing:
input:
expand("data/sequencing_genomic/{{hostcode}}_R{PE}.fastq.gz", PE=DIRECTIONS)
params:
"LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:36"
output:
p1=temp("data/sequencing_genomic_trimmed/{hostcode}_R1.fastq.gz"),
p2=temp("data/sequencing_genomic_trimmed/{hostcode}_R2.fastq.gz")
threads: 4
resources: io=1
log:
stdout="logs/trimmomatic_genomicsequencing.{hostcode}.stdout",
stderr="logs/trimmomatic_genomicsequencing.{hostcode}.stderr",
log="logs/trimmomatic_genomicsequencing.{hostcode}.log",
summary="logs/trimmomatic_genomicsequencing_summary{hostcode}.log"
shell:
"trimmomatic PE -threads {threads} -trimlog {log.log} -summary {log.summary} {input} {output.p1} /dev/null {output.p2} /dev/null {params} > {log.stdout} 2> {log.stderr}"
rule filter_for_host:
input:
expand("references/host_genome/host_filter_bt2index/host_filter.{i}.bt2",i=range(1,4)),
expand("references/host_genome/host_filter_bt2index/host_filter.rev.{i}.bt2",i=range(1,2)),
s1=expand("data/sequencing_genomic_trimmed/{{hostcode}}_R{PE}.fastq.gz",PE=1),
s2=expand("data/sequencing_genomic_trimmed/{{hostcode}}_R{PE}.fastq.gz",PE=2)
params:
opts="--very-fast",
i="references/host_genome/host_filter_bt2index/host_filter",
outbase="data/sequencing_genomic_trimmed_filtered/{hostcode}"
output:
temp(expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}",PE=DIRECTIONS))
threads: 100
log:
stderr="logs/bowtie2filterforhost{hostcode}.stderr"
shell:
"bowtie2 {params.opts} --threads {threads} --un-conc-gz {params.outbase} -x {params.i} -1 {input.s1} -2 {input.s2} > /dev/null 2> {log.stderr}"
rule filter_for_host_rename:
input:
reads=expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}",PE=DIRECTIONS),
s1=expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}",PE=1),
s2=expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}",PE=2)
output:
reads=expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}.fastq.gz",PE=DIRECTIONS),
s1=expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}.fastq.gz",PE=1),
s2=expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}.fastq.gz",PE=2)
shell:
"mv {input.s1} {output.s1} && mv {input.s2} {output.s2}"
rule spades_hammer:
input:
reads=expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}.fastq.gz",PE=DIRECTIONS),
s1=expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}.fastq.gz",PE=1),
s2=expand("data/sequencing_genomic_trimmed_filtered/{{hostcode}}.{PE}.fastq.gz",PE=2)
params:
options="--only-error-correction",
basedir=lambda w: expand("data/sequencing_genomic_trimmed_filtered_corrected/{hostcode}/",hostcode=w.hostcode)
output:
reads=expand("data/sequencing_genomic_trimmed_filtered_corrected/{{hostcode}}/corrected/{{hostcode}}.{PE}.fastq.00.0_0.cor.fastq.gz",PE=DIRECTIONS)
threads: 100
log:
stdout="logs/SPAdes_correct_sequencing{hostcode}.stdout",
stderr="logs/SPAdes_correct_sequencing{hostcode}.stderr"
shell:
"spades.py {params.options} -t {threads} -1 {input.s1} -2 {input.s2} -o {params.basedir} > {log.stdout} 2> {log.stderr}"
rule spades_first_assembly:
input:
s1=ancient(expand("data/sequencing_genomic_trimmed_filtered_corrected/{{hostcode}}/corrected/{{hostcode}}.{PE}.fastq.00.0_0.cor.fastq.gz",PE=1)),
s2=ancient(expand("data/sequencing_genomic_trimmed_filtered_corrected/{{hostcode}}/corrected/{{hostcode}}.{PE}.fastq.00.0_0.cor.fastq.gz",PE=2))
params:
basedir= lambda w: expand("data/assembly_{assemblytype}/{hostcode}/", hostcode=w.hostcode, assemblytype='singles_hostfiltered'),
options="--meta --only-assembler"
output:
contigs=expand("data/assembly_{assemblytype}/{{hostcode}}/{assemblyfile}.fasta",assemblytype='singles_hostfiltered',assemblyfile='contigs'),
scaffolds=expand("data/assembly_{assemblytype}/{{hostcode}}/{assemblyfile}.fasta",assemblytype='singles_hostfiltered',assemblyfile='scaffolds')
threads: 100
shadow: "shallow"
resources:
mem_mb=500
log:
stdout=expand("logs/SPADES_assembly_{assemblytype}_{{hostcode}}.stdout",assemblytype='singles_hostfiltered'),
stderr=expand("logs/SPADES_assembly_{assemblytype}_{{hostcode}}.stderr",assemblyfile='contigs',assemblytype='singles_hostfiltered')
shell:
"spades.py {params.options} -t {threads} -m {resources.mem_mb} -1 {input.s1} -2 {input.s2} -o {params.basedir} > {log.stdout} 2> {log.stderr}"
## process assembly for taxonomy including a taxonomy based second filter
rule CAT_prepare_ORFS:
input:
assembly="data/assembly_{assemblytype}/{hostcode}/{assemblyfile}.fasta"
output:
p="data/assembly_{assemblytype}/{hostcode}/{assemblyfile}_predicted_proteins.fasta",
g="data/assembly_{assemblytype}/{hostcode}/{assemblyfile}_predicted_proteins.gff"
params:
"-p meta -g 11 -q -f gff"
threads: 1
log:
stdout="logs/CAT_assembly_{assemblytype}_{assemblyfile}_prodigal_{hostcode}.stdout",
stderr="logs/CAT_assembly_{assemblytype}_{assemblyfile}_prodigal_{hostcode}.stderr"
shell:
"prodigal -i {input.assembly} -a {output.p} -o {output.g} {params} 2> {log.stderr} > {log.stdout}"
rule CAT_classify_contigs_assembly:
input:
assembly="data/assembly_{assemblytype}/{hostcode}/{assemblyfile}.fasta",
dmnd="references/CAT_customised_20190108/CAT_database_customised/2019-03-27.nr.dmnd",
db="references/CAT_customised_20190108/CAT_database_customised",
tf="references/CAT_customised_20190108/taxonomy_customised",
p="data/assembly_{assemblytype}/{hostcode}/{assemblyfile}_predicted_proteins.fasta"
output:
i="data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}.contig2classification.txt",
# g=expand("data/assembly_{assemblytype}/{{hostcode}}/CAT_{{hostcode}}.predicted_proteins.gff",assemblytype='singles_hostfiltered'),
# f=expand("data/assembly_{assemblytype}/{{hostcode}}/CAT_{{hostcode}}.predicted_proteins.faa",assemblytype='singles_hostfiltered'),
o="data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}.ORF2LCA.txt",
l="data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}.log"
shadow: 'shallow'
params:
b = lambda w: expand("data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}", assemblytype=w.assemblytype, hostcode=w.hostcode, assemblyfile=w.assemblyfile),
options = '-r 5'
threads: 100
resources:
mem_mb=30000
log:
stdout="logs/CAT_assembly_{assemblytype}_{assemblyfile}_classification_{hostcode}.stdout",
stderr="logs/CAT_assembly_{assemblytype}_{assemblyfile}_classification_{hostcode}.stderr"
shell:
"CAT contigs {params.options} -c {input.assembly} -d {input.db} -p {input.p} -t {input.tf} --out_prefix {params.b} -n {threads} 2> {log.stderr} > {log.stdout}"
rule CAT_add_names_assembly:
input:
i="data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}.contig2classification.txt",
tf="references/CAT_customised_20190108/taxonomy_customised"
output:
"data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}_taxonomy.tab"
params:
"--only_official"
log:
stdout="logs/CAT_assembly_{assemblytype}_{assemblyfile}_classification_taxonomy_{hostcode}.stdout",
stderr="logs/CAT_assembly_{assemblytype}_{assemblyfile}_classification_taxonomy_{hostcode}.stderr"
threads: 1
shell:
"CAT add_names {params} -i {input.i} -t {input.tf} -o {output} > {log.stdout} 2> {log.stderr}"
rule CAT_filter_contignames_first_spades_assembly:
input:
expand("data/assembly_{{assemblytype}}/{{hostcode}}/CAT_{{hostcode}}_{assemblyfile}_taxonomy.tab",assemblyfile='scaffolds')
output:
expand("data/assembly_{{assemblytype}}/{{hostcode}}/CAT_{{hostcode}}_{assemblyfile}_filterlist.txt",assemblyfile='scaffolds')
threads: 1
log:
expand("logs/CAT_assembly_{{assemblytype}}_{assemblyfile}filterlist_{{hostcode}}.stderr",assemblyfile='scaffolds')
shell:
"cat {input} | grep -v Eukaryota | cut -f 1 | sort -n > {output} 2> {log}"
rule BAT_filter_contignames_bins:
input:
"data/bins_{assemblytype}/{hostcode}.BAT.names.txt"
output:
"data/assembly_{assemblytype}/{hostcode}/BAT_{hostcode}_filterlist.txt"
params:
binfolder = "data/bins_{assemblytype}/{hostcode}"
log:
"logs/BAT_filter_contignames_bins_{assemblytype}_{hostcode}"
shell:
"""
for f in $(cat {input} | grep Eukaryota | cut -f 1)
do grep '>' {params.binfolder}/$f.fa
done | tr -d '>' | cut -f 1 > {output} 2> {log}
"""
rule combine_filter_contignames:
input:
"data/assembly_{assemblytype}/{hostcode}/BAT_{hostcode}_filterlist.txt",
expand("data/assembly_{{assemblytype}}/{{hostcode}}/CAT_{{hostcode}}_{assemblyfile}_filterlist.txt",assemblyfile='scaffolds')
output:
expand("data/assembly_{{assemblytype}}/{{hostcode}}/combined_filterlist_{{hostcode}}_{assemblyfile}.tab",assemblyfile='scaffolds')
shell:
"cat {input} | cut -f 1 | sort | uniq > {output}"
rule create_filter_fasta_first_spades_assembly:
input:
n=expand("data/assembly_{{assemblytype}}/{{hostcode}}/combined_filterlist_{{hostcode}}_{assemblyfile}.tab",assemblyfile='scaffolds'),
f=expand("data/assembly_{{assemblytype}}/{{hostcode}}/{assemblyfile}_short_names.fasta",assemblyfile='scaffolds')
output:
"data/assembly_{assemblytype}/{hostcode}/CAT_BAT_filter_{hostcode}.fasta"
threads: 1
log:
stdout="logs/CAT_create_assembly_{assemblytype}_filter_{hostcode}.stdout",
stderr="logs/CAT_create_assembly_{assemblytype}_filter_{hostcode}.stderr"
shell:
"samtools faidx {input.f} -o {output} -r {input.n} > {log.stdout} 2> {log.stderr}"
rule create_first_spades_assembly_filter_bt2_index:
input:
"data/assembly_{assemblytype}/{hostcode}/CAT_BAT_filter_{hostcode}.fasta"
params:
filter = lambda w: expand("data/assembly_{assemblytype}/{hostcode}/CAT_BAT_filter_bt2index_{hostcode}/{hostcode}_filter",assemblytype=w.assemblytype, hostcode=w.hostcode)
output:
expand("data/assembly_{{assemblytype}}/{{hostcode}}/CAT_BAT_filter_bt2index_{{hostcode}}/{{hostcode}}_filter.{i}.bt2",i=range(1,4)),
expand("data/assembly_{{assemblytype}}/{{hostcode}}/CAT_BAT_filter_bt2index_{{hostcode}}/{{hostcode}}_filter.rev.{i}.bt2",i=range(1,2))
threads: 12
log:
stdout="logs/CAT_create_assembly_filter_{assemblytype}_filterbt2index_{hostcode}.stdout",
stderr="logs/CAT_create_assembly_filter_{assemblytype}_filterbt2index_{hostcode}.stderr"
shell:
"bowtie2-build --threads {threads} {input} {params.filter} > {log.stdout} 2> {log.stderr}"
rule filter_for_assembly:
input:
expand("data/assembly_{assemblytype}/{{hostcode}}/CAT_BAT_filter_bt2index_{{hostcode}}/{{hostcode}}_filter.{i}.bt2",i=range(1,4),assemblytype='singles_hostfiltered'),
expand("data/assembly_{assemblytype}/{{hostcode}}/CAT_BAT_filter_bt2index_{{hostcode}}/{{hostcode}}_filter.rev.{i}.bt2",i=range(1,2),assemblytype='singles_hostfiltered'),
s1=expand("data/sequencing_genomic_trimmed_filtered_corrected/{{hostcode}}/corrected/{{hostcode}}.{PE}.fastq.00.0_0.cor.fastq.gz",PE=1,),
s2=expand("data/sequencing_genomic_trimmed_filtered_corrected/{{hostcode}}/corrected/{{hostcode}}.{PE}.fastq.00.0_0.cor.fastq.gz",PE=2)
params:
opts="--very-sensitive",
i = lambda w : expand("data/assembly_{assemblytype}/{hostcode}/CAT_BAT_filter_bt2index_{hostcode}/{hostcode}_filter",assemblytype='singles_hostfiltered', hostcode = w.hostcode),
outbase= lambda w : expand("data/sequencing_doublefiltered/{hostcode}/{hostcode}", hostcode=w.hostcode)
output:
b1= expand("data/sequencing_doublefiltered/{{hostcode}}/{{hostcode}}.{PE}.fastq.gz",PE=1),
b2= expand("data/sequencing_doublefiltered/{{hostcode}}/{{hostcode}}.{PE}.fastq.gz",PE=2),
sin="data/sequencing_doublefiltered/{hostcode}/{hostcode}.singletons.fastq.gz"
threads: 36
log:
stderr="logs/bowtie2_filter_for_assembly_doublefilter_{hostcode}.stderr",
samstderr="logs/bowtie2_filter_for_assembly_doublefilter_{hostcode}_samtoolsfastq.stderr",
samstdout="logs/bowtie2_filter_for_assembly_doublefilter_{hostcode}_samtoolsfastq.stdout"
shell:
"""
bowtie2 {params.opts} --threads {threads} \
-x {params.i} \
-1 {input.s1} \
-2 {input.s2} \
2> {log.stderr} \
| samtools fastq -f 13 \
-@ {threads} \
-n -c 9 \
-1 {output.b1} \
-2 {output.b2} \
-0 {output.sin} \
- \
2> {log.samstderr} \
> {log.samstdout}
"""
## double filtered assemblies
rule spades_second_assembly:
input:
reads=expand("data/sequencing_doublefiltered/{{hostcode}}/{{hostcode}}.{PE}.fastq.gz",PE=DIRECTIONS),
s1=expand("data/sequencing_doublefiltered/{{hostcode}}/{{hostcode}}.{PE}.fastq.gz",PE=1),
s2=expand("data/sequencing_doublefiltered/{{hostcode}}/{{hostcode}}.{PE}.fastq.gz",PE=2)
params:
options="--meta --only-assembler",
basedir=lambda w: expand("data/assembly_{assemblytype}/{hostcode}/",assemblytype='singles_doublefiltered',hostcode=w.hostcode)
output:
contigs=protected(expand("data/assembly_{assemblytype}/{{hostcode}}/contigs.fasta",assemblytype='singles_doublefiltered')),
scaffolds=protected(expand("data/assembly_{assemblytype}/{{hostcode}}/scaffolds.fasta",assemblytype='singles_doublefiltered')),
graph=protected(expand("data/assembly_{assemblytype}/{{hostcode}}/assembly_graph.fastg",assemblytype='singles_doublefiltered')),
graph_scaffolds=protected(expand("data/assembly_{assemblytype}/{{hostcode}}/assembly_graph_with_scaffolds.gfa",assemblytype='singles_doublefiltered')),
datasetyaml=protected(expand("data/assembly_{assemblytype}/{{hostcode}}/input_dataset.yaml",assemblytype='singles_doublefiltered')),
paramfile=protected(expand("data/assembly_{assemblytype}/{{hostcode}}/params.txt",assemblytype='singles_doublefiltered'))
threads: 100
shadow: "shallow"
resources:
mem_mb=500
log:
stdout=expand("logs/SPADES_assembly_{assemblytype}_{{hostcode}}.stdout",assemblytype='singles_doublefiltered'),
stderr=expand("logs/SPADES_assembly_{assemblytype}_{{hostcode}}.stderr",assemblytype='singles_doublefiltered')
shell:
"spades.py {params.options} -t {threads} -m {resources.mem_mb} -1 {input.s1} -2 {input.s2} -o {params.basedir} > {log.stdout} 2> {log.stderr}"
## assembly analyses and diagnostigs
rule collect_assembly_stats_singles:
input:
expand("data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}_taxonomy.tab",assemblytype=ASSEMBLYTYPES,hostcode=HOSTCODES,assemblyfile=ASSEMBLYFILES)
params:
assemblytype= lambda w : expand("{assemblytype}",assemblytype=ASSEMBLYTYPES),
hostcode= lambda w : expand("{hostcode}",hostcode=HOSTCODES),
assemblyfile= lambda w : expand("{assemblyfile}",assemblyfile=ASSEMBLYFILES)
output:
"analyses/assembly_stats_and_taxonomy.tab"
threads: 12
resources:
mem_mb=1000
shell:
"""
scripts/make_assembly_stats_and_taxonomy.bash "{params.assemblytype}" "{params.hostcode}" "{params.assemblyfile}" {threads} {resources.mem_mb} {output}
"""
rule collect_assembly_stats_hybrid:
input:
expand("data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}_taxonomy.tab",assemblytype='hybrid_doublefiltered',hostcode=HOSTS,assemblyfile=ASSEMBLYFILES)
params:
assemblytype= lambda w : expand("{assemblytype}",assemblytype='hybrid_doublefiltered'),
hostcode= lambda w : expand("{hostcode}",hostcode=HOSTS),
assemblyfile= lambda w : expand("{assemblyfile}",assemblyfile=ASSEMBLYFILES)
output:
"analyses/assembly-hybrid_stats_and_taxonomy.tab"
threads: 12
resources:
mem_mb=1000
shell:
"""
scripts/make_assembly_stats_and_taxonomy.bash "{params.assemblytype}" "{params.hostcode}" "{params.assemblyfile}" {threads} {resources.mem_mb} {output}
"""
## assembly processing for binning an Anvi'o
ruleorder: shorten_scaffold_names_awk > shorten_scaffold_names_anvi
rule shorten_scaffold_names_awk:
input:
scaffolds=expand("data/assembly_{assemblytype}/{{hostcode}}/{{assemblyfile}}.fasta",assemblytype='singles_hostfiltered')
output:
scaffolds=expand("data/assembly_{assemblytype}/{{hostcode}}/{{assemblyfile}}_short_names.fasta",assemblytype='singles_hostfiltered')
shell:
"""awk -F '_' '/>NODE/{{$0=">NODE_"$2}}1' {input} > {output}"""
rule CAT_filter_unclassified_and_eukaryotic_scaffolds_for_anvio:
input:
expand("data/assembly_{{assemblytype}}/{{hostcode}}/CAT_{{hostcode}}_{assemblyfile}_taxonomy.tab",assemblyfile='scaffolds')
output:
expand("data/assembly_{{assemblytype}}/{{hostcode}}/CAT_{{hostcode}}_{assemblyfile}_minus-unclassified_minus-eukaryotic_filterlist.txt",assemblyfile='scaffolds')
threads: 1
log:
expand("logs/CAT_assembly_{{assemblytype}}_{assemblyfile}filterlist_{{hostcode}}.stderr",assemblyfile='scaffolds')
shell:
"cat {input} | grep -v Eukaryota | grep -v unclassified | grep -v '#' | cut -f 1 | sort -n > {output} 2> {log}"
rule filter_unclassfied_filter_eukaryotic:
input:
scaffolds="data/assembly_{assemblytype}/{hostcode}/{assemblyfile}.fasta",
filterlist=expand("data/assembly_{{assemblytype}}/{{hostcode}}/CAT_{{hostcode}}_{assemblyfile}_minus-unclassified_minus-eukaryotic_filterlist.txt",assemblyfile='scaffolds')
output:
scaffolds="data/assembly_{assemblytype}/{hostcode}/{assemblyfile}_minus-unclassified_minus-eukaryotic.fasta"
log:
stdout="logs/filter-final-fasta-eukaryotic-unclassfied_{assemblytype}_{hostcode}_{assemblyfile}.stdout",
stderr="logs/filter-final-fasta-eukaryotic-unclassified_{assemblytype}_{hostcode}_{assemblyfile}.stderr"
shell:
"samtools faidx {input.scaffolds} -o {output.scaffolds} -r {input.filterlist} > {log.stdout} 2> {log.stderr}"
rule shorten_scaffold_names_anvi:
input:
scaffolds="data/assembly_{assemblytype}/{hostcode}/{assemblyfile}_minus-unclassified_minus-eukaryotic.fasta"
output:
scaffolds="data/assembly_{assemblytype}/{hostcode}/{assemblyfile}_short_names.fasta"
log:
report="logs/anvi-script-reformat-fasta_{assemblytype}_{hostcode}_{assemblyfile}.report",
stdout="logs/anvi-script-reformat-fasta_{assemblytype}_{hostcode}_{assemblyfile}.stdout",
stderr="logs/anvi-script-reformat-fasta_{assemblytype}_{hostcode}_{assemblyfile}.stderr"
conda:
"envs/anvio.yaml"
shell:
"anvi-script-reformat-fasta -l 2500 --simplify-names -r {log.report} {input} -o {output} > {log.stdout} 2> {log.stderr} "
rule bwa_index_assembly_scaffolds:
input:
scaffolds=expand("data/assembly_{{assemblytype}}/{{hostcode}}/{assemblyfile}_short_names.fasta",assemblyfile='scaffolds')
params:
outbase=lambda w: expand("data/assembly_{assemblytype}/{hostcode}/scaffolds_bwa_index/{assemblyfile}",assemblyfile='scaffolds',assemblytype=w.assemblytype,hostcode=w.hostcode)
output:
expand("data/assembly_{{assemblytype}}/{{hostcode}}/scaffolds_bwa_index/scaffolds.{ext}",ext=['bwt','pac','ann','sa','amb'])
threads: 1
log:
stdout="logs/bwa_index_{assemblytype}_{hostcode}.stdout",
stderr="logs/bwa_index_{assemblytype}_{hostcode}.stderr"
shell:
"bwa index -p {params.outbase} {input} > {log.stdout} 2> {log.stderr}"
import os.path
def get_binning_reads(wildcards):
index={'index': expand("data/assembly_{{assemblytype}}/{{hostcode}}/scaffolds_bwa_index/scaffolds.{ext}",ext=['bwt','pac','ann','sa','amb']) }
if wildcards.assemblytype != 'hybrid_doublefiltered' :
pathpe=("data/sequencing_binning_signals/" + wildcards.binningsignal + ".trimmed_paired.R1.fastq.gz")
pathse=("data/sequencing_binning_signals/" + wildcards.binningsignal + ".trimmed.fastq.gz")
if os.path.isfile(pathpe) == True :
dict = {'reads' : expand("data/sequencing_binning_signals/{binningsignal}.trimmed_paired.R{PE}.fastq.gz", PE=[1,2],binningsignal=wildcards.binningsignal) }
elif os.path.isfile(pathse) == True :
dict = {'reads' : expand("data/sequencing_binning_signals/{binningsignal}.trimmed.fastq.gz", binningsignal=wildcards.binningsignal) }
return dict
dict.update(index)
return dict
elif wildcards.assemblytype == 'hybrid_doublefiltered' :
if len(list(filter(lambda x:wildcards.binningsignal in x, BINNINGSIGNALS))) > 0 :
pathpe=("data/sequencing_binning_signals/" + wildcards.binningsignal + ".trimmed_paired.R1.fastq.gz")
pathse=("data/sequencing_binning_signals/" + wildcards.binningsignal + ".trimmed.fastq.gz")
index={'index': expand("data/assembly_{{assemblytype}}/{{hostcode}}/scaffolds_bwa_index/scaffolds.{ext}",ext=['bwt','pac','ann','sa','amb']) }
if os.path.isfile(pathpe) == True :
dict = {'reads' : expand("data/sequencing_binning_signals/{binningsignal}.trimmed_paired.R{PE}.fastq.gz", PE=[1,2],binningsignal=wildcards.binningsignal) }
elif os.path.isfile(pathse) == True :
dict = {'reads' : expand("data/sequencing_binning_signals/{binningsignal}.trimmed.fastq.gz", binningsignal=wildcards.binningsignal) }
return dict
dict.update(index)
elif len(list(filter(lambda x:wildcards.binningsignal in x, BINNINGSIGNALS))) == 0 :
dict = { 'reads' : expand("data/sequencing_genomic_trimmed/{hostcode}_R{PE}.fastq.gz",PE=DIRECTIONS,hostcode=wildcards.binningsignal) }
dict.update(index)
return dict
dict.update(index)
return dict
rule backmap_bwa_mem:
input:
unpack(get_binning_reads),
expand("data/assembly_{{assemblytype}}/{{hostcode}}/scaffolds_bwa_index/scaffolds.{ext}",ext=['bwt','pac','ann','sa','amb'])
params:
index=lambda w: expand("data/assembly_{assemblytype}/{hostcode}/scaffolds_bwa_index/scaffolds",assemblytype=w.assemblytype,hostcode=w.hostcode)
output:
temp("data/assembly_{assemblytype}_binningsignals/{hostcode}/{hostcode}+{binningsignal}.bam")
threads: 100
log:
stdout="logs/bwa_backmap_samtools_{assemblytype}_{hostcode}_{binningsignal}.stdout",
samstderr="logs/bwa_backmap_samtools_{assemblytype}_{hostcode}_{binningsignal}.stdout",
stderr="logs/bwa_backmap_{assemblytype}_{hostcode}_{binningsignal}.stderr"
shell:
"bwa mem -t {threads} {params.index} {input.reads} 2> {log.stderr} | samtools view -F 4 -@ {threads} -b -o {output} 2> {log.samstderr} > {log.stdout}"
# def get_source_binning_reads(wildcards):
# if wildcards.assemblytype != 'hybrid_doublefiltered':
# s1={'s1' : expand("data/sequencing_genomic_trimmed/{hostcode}_R{PE}.fastq.gz",PE=1,hostcode=wildcards.hostcode) }
# s2={'s2' : expand("data/sequencing_genomic_trimmed/{hostcode}_R{PE}.fastq.gz",PE=2,hostcode=wildcards.hostcode) }
# index={'index' : expand("data/assembly_{assemblytype}/{hostcode}/scaffolds_bwa_index/scaffolds.{ext}",ext=['bwt','pac','ann','sa','amb'],hostcode=wildcards.hostcode,assemblytype=wildcards.assemblytype)}
# input={}
# input.update(s1)
# input.update(s2)
# input.update(index)
# (input)
# elif wildcards.assemblytype == 'hybrid_doublefiltered':
# s1={'s1' : expand("data/sequencing_genomic_trimmed/{hostcode}_R{PE}.fastq.gz",PE=1,hostcode=wildcards.hostcode) }
# s2={'s2' : expand("data/sequencing_genomic_trimmed/{hostcode}_R{PE}.fastq.gz",PE=2,hostcode=wildcards.hostcode) }
# index={'index' : expand("data/assembly_{assemblytype}/{host}/scaffolds_bwa_index/scaffolds.{ext}",ext=['bwt','pac','ann','sa','amb'],host=wildcards.hostcode,assemblytype=wildcards.assemblytype)}
# input={}
# input.update(s1)
# input.update(s2)
# input.update(index)
# return(input)
# return(input)
ruleorder: BLASR_backmap_long_reads > backmap_bwa_mem_assemblysource
rule BLASR_backmap_long_reads:
input:
reads="data/sequencing_genomic-longreads_trimmed/Azfil_lab_longreads-selfcorrected_trimmed.fasta",
scaffolds=expand("data/assembly_{{assemblytype}}/{{hostcode}}/{assemblyfile}_short_names.fasta",assemblyfile='scaffolds')
output:
temp("data/assembly_{assemblytype}_binningsignals/{hostcode}/{hostcode}+pacbio_reads.bam")
threads: 100
params:
"--hitPolicy allbest --bam"
shadow: "shallow"
conda:
"envs/blasr.yaml"
log:
stdout="logs/BLASR_filter_long_reads_{assemblytype}_{hostcode}.stdout",
stderr="logs/BLASR_filter_long_reads_{assemblytype}_{hostcode}.stderr"
shell:
"blasr {input.reads} {input.scaffolds} {params} --nproc {threads} --out {output} > {log.stdout} 2> {log.stderr}"
rule backmap_bwa_mem_assemblysource:
input:
#unpack(get_source_binning_reads)
s1=expand("data/sequencing_genomic_trimmed/{{hostcode}}_R{PE}.fastq.gz",PE=1),
s2=expand("data/sequencing_genomic_trimmed/{{hostcode}}_R{PE}.fastq.gz",PE=2),
index=expand("data/assembly_{{assemblytype}}/{{hostcode}}/scaffolds_bwa_index/scaffolds.{ext}",ext=['bwt','pac','ann','sa','amb'])
params:
index=lambda w: expand("data/assembly_{assemblytype}/{hostcode}/scaffolds_bwa_index/scaffolds",assemblytype=w.assemblytype,hostcode=w.hostcode)
output:
temp("data/assembly_{assemblytype}_binningsignals/{hostcode}/{hostcode}+{hostcode}.bam")
threads: 100
log:
stdout="logs/bwa_backmap_samtools_{assemblytype}_{hostcode}.stdout",
samstderr="logs/bwa_backmap_samtools_{assemblytype}_{hostcode}.stdout",
stderr="logs/bwa_backmap_{assemblytype}_{hostcode}.stderr"
shell:
"bwa mem -t {threads} {params.index} {input.s1} {input.s2} 2> {log.stderr} | samtools view -F 4 -@ {threads} -b -o {output} 2> {log.samstderr} > {log.stdout}"
rule backmap_samtools_sort:
input:
"data/assembly_{assemblytype}_binningsignals/{hostcode}/{hostcode}+{binningsignal}.bam"
output:
"data/assembly_{assemblytype}_binningsignals/{hostcode}/{hostcode}+{binningsignal}.sorted.bam"
threads: 100
resources:
mem_mb=2000
log:
stdout="logs/bwa_backmap_samtools_sort_{assemblytype}_{hostcode}_{binningsignal}.stdout",
stderr="logs/bwa_backmap_samtools_sort_{assemblytype}_{hostcode}_{binningsignal}.stderr"
shell:
"samtools sort -@ {threads} -m {resources.mem_mb}M -o {output} {input} > {log.stdout} 2> {log.stderr}"
rule backmap_samtools_index_binningsignal:
input:
"data/assembly_{assemblytype}_binningsignals/{hostcode}/{hostcode}+{binningsignal}.sorted.bam"
output:
"data/assembly_{assemblytype}_binningsignals/{hostcode}/{hostcode}+{binningsignal}.sorted.bam.bai"
log:
stdout="logs/bwa_backmap_samtools_index_{assemblytype}_{hostcode}_{binningsignal}.stdout",
stderr="logs/bwa_backmap_samtools_index_{assemblytype}_{hostcode}_{binningsignal}.stderr"
threads: 100
shell:
"samtools index -@ {threads} {input} > {log.stdout} 2> {log.stderr}"
def get_bams_for_binning(wildcards):
if wildcards.assemblytype != 'hybrid_doublefiltered':
input=expand("data/assembly_{assemblytype}_binningsignals/{hostcode}/{hostcode}+{hostcode}.sorted.bam",assemblytype=wildcards.assemblytype,hostcode=wildcards.hostcode) + expand("data/assembly_{assemblytype}_binningsignals/{hostcode}/{hostcode}+{binningsignal}.sorted.bam",binningsignal=BINNINGSIGNALS,assemblytype=wildcards.assemblytype,hostcode=wildcards.hostcode)
return(input)
elif wildcards.assemblytype == 'hybrid_doublefiltered':
HOST_LIBRARIES=list(filter(lambda x:wildcards.hostcode in x, HOSTCODES)) + BINNINGSIGNALS
input=expand("data/assembly_{assemblytype}_binningsignals/{host}/{host}+{hostcode}.sorted.bam",assemblytype=wildcards.assemblytype,host=wildcards.hostcode,hostcode=HOST_LIBRARIES)
return(input)
rule jgi_summarize_script:
input:
get_bams_for_binning
output:
"data/assembly_{assemblytype}/{hostcode}/{hostcode}_depthmatrix.tab"
log:
stdout="logs/jgi_summarize_script_{assemblytype}_{hostcode}.stdout",
stderr="logs/jgi_summarize_script_{assemblytype}_{hostcode}.stdout"
threads: 32
shell:
"jgi_summarize_bam_contig_depths --minContigLength 2500 --percentIdentity 80 --outputDepth {output} {input} > {log.stdout} 2> {log.stderr}"
checkpoint metabat2:
input:
scaffolds="data/assembly_{assemblytype}/{hostcode}/scaffolds_short_names.fasta",
depthmatrix="data/assembly_{assemblytype}/{hostcode}/{hostcode}_depthmatrix.tab"
output:
bins=directory("data/bins_{assemblytype}/{hostcode,[A-Za-z0-9_]+}")
params:
prefix=lambda w: expand("data/bins_{assemblytype}/{hostcode}/{hostcode}_bin",assemblytype=w.assemblytype,hostcode=w.hostcode)
threads: 72
log:
stdout="logs/metabat2_{assemblytype}_{hostcode}.stdout",
stderr="logs/metabat2_{assemblytype}_{hostcode}.stdout"
shell:
"metabat2 -t {threads} -i {input.scaffolds} -a {input.depthmatrix} -o {params.prefix} > {log.stdout} 2> {log.stderr}"
rule checkm_set_data_folder:
input:
"references/checkm_data"
output:
touch("references/checkm_data_setroot.done")
conda:
"envs/checkm.yaml"
shell:
"checkm data setRoot {input}"
rule checkm:
input:
bins="data/bins_{assemblytype}/{hostcode}",
set_root="references/checkm_data_setroot.done"
output:
table="data/bins_{assemblytype}_checkm/{hostcode}/{hostcode}.checkm_out"
params:
options="-x fa --pplacer_threads=12 --tab_table",
dir=lambda w:expand("data/bins_{assemblytype}_checkm/{hostcode}",assemblytype=w.assemblytype,hostcode=w.hostcode)
threads: 72
log:
stdout="logs/checkm_{assemblytype}_{hostcode}.stdout",
stderr="logs/checkm_{assemblytype}_{hostcode}.stderr"
conda:
"envs/checkm.yaml"
shell:
"""
if [ -d {params.dir} ]
then rm -rf {params.dir}
fi
checkm lineage_wf -t {threads} {params.options} {input.bins} {params.dir} -f {output.table} > {log.stdout} 2> {log.stderr}
"""
rule prodigal_get_ORFs_for_CAT_bins:
input:
bindir="data/bins_{assemblytype}/{hostcode}"
output:
a="data/bins_{assemblytype}/{hostcode}.BAT.concatenated.predicted_proteins.faa",
o="data/bins_{assemblytype}/{hostcode}.BAT.concatenated.predicted_proteins.gff"
params:
"-p meta -g 11 -q -f gff"
shell:
"prodigal -i <(cat {input}/*.fa ) -a {output.a} -o {output.o} {params}"
rule CAT_bins:
input:
# a="data/bins_{assemblytype}/{hostcode}.BAT.concatenated.predicted_proteins.faa",
# o="data/bins_{assemblytype}/{hostcode}.BAT.concatenated.predicted_proteins.gff",
bindir="data/bins_{assemblytype}/{hostcode}",
dmnd="references/CAT_customised_20190108/CAT_database_customised/2019-03-27.nr.dmnd",
db="references/CAT_customised_20190108/CAT_database_customised",
tf="references/CAT_customised_20190108/taxonomy_customised"
output:
"data/bins_{assemblytype}/{hostcode}.BAT.bin2classification.txt"
# shadow: 'shallow'
params:
options= " -s '.fa' ",
prefix=lambda w : expand( "data/bins_{assemblytype}/{hostcode}.BAT" , assemblytype=w.assemblytype , hostcode=w.hostcode )
threads: 72
log:
stdout="logs/BAT_{assemblytype}_{hostcode}.stdout",
stderr="logs/BAT_{assemblytype}_{hostcode}.stderr"
shell:
"CAT bins -n {threads} -b {input.bindir} -d {input.db} -t {input.tf} {params.options} -o {params.prefix} > {log.stdout} 2> {log.stderr}"
rule BAT_add_names:
input:
i="data/bins_{assemblytype}/{hostcode}.BAT.bin2classification.txt",
tf="references/CAT_customised_20190108/taxonomy_customised"
output:
"data/bins_{assemblytype}/{hostcode}.BAT.names.txt",
params:
"--only_official"
log:
stdout="logs/BAT_assembly_{assemblytype}_classification_taxonomy_{hostcode}.stdout",
stderr="logs/BAT_assembly_{assemblytype}_classification_taxonomy_{hostcode}.stderr"
threads: 1
shell:
"CAT add_names {params} -i {input.i} -t {input.tf} -o {output} > {log.stdout} 2> {log.stderr}"
rule anvi_gen_contigs_database:
input:
scaffolds="data/assembly_{assemblytype}/{hostcode}/scaffolds_short_names.fasta"
output:
db="data/assembly_{assemblytype}_anvio/{hostcode}/{hostcode}_contigs.db"
log:
stdout="logs/anvi-gen-contigs-database_{assemblytype}_{hostcode}.stdout",
stderr="logs/anvi-gen-contigs-database_{assemblytype}_{hostcode}.stderr"
params:
"-n 'sample {hostcode} assembly {assemblytype}'"
conda:
"envs/anvio.yaml"
shell:
"""
anvi-gen-contigs-database -f {input} -o {output} {params} > {log.stdout} 2> {log.stderr}
"""
rule anvi_run_hmms:
input:
db="data/assembly_{assemblytype}_anvio/{hostcode}/{hostcode}_contigs.db"
output:
touch("data/assembly_{assemblytype}_anvio/{hostcode}/{hostcode}_contigs_db_run_hmms.done")
threads: 5
log:
stdout="logs/anvi-run-hmms_{assemblytype}_{hostcode}.stdout",
stderr="logs/anvi-run-hmms_{assemblytype}_{hostcode}.stderr"
conda:
"envs/anvio.yaml"
shell:
"anvi-run-hmms -c {input} -T {threads} > {log.stdout} 2> {log.stderr}"
rule anvi_setup_ncbi_cogs:
output:
dir=directory("references/anvi_ncbi_cogs")
threads: 100
log:
stdout="logs/anvi-setup-cogs.stdout",
stderr="logs/anvi-setup-cogs.stderr"
conda:
"envs/anvio.yaml"
shell:
"anvi-setup-ncbi-cogs -T {threads} --just-do-it --cog-data-dir {output.dir} > {log.stdout} 2> {log.stderr}"
rule anvi_run_ncbi_cogs:
input:
db="data/assembly_{assemblytype}_anvio/{hostcode}/{hostcode}_contigs.db",
dir="references/anvi_ncbi_cogs"
output:
touch("data/assembly_{assemblytype}_anvio/{hostcode}/{hostcode}_contigs_db_run_ncbi_cogs.done")
threads: 20
params: "--sensitive"
log:
stdout="logs/anvi-run-cogs_{assemblytype}_{hostcode}.stdout",
stderr="logs/anvi-run-cogs_{assemblytype}_{hostcode}.stderr"
conda:
"envs/anvio.yaml"
shell:
"anvi-run-ncbi-cogs {params} -c {input.db} -T {threads} --cog-data-dir {input.dir} > {log.stdout} 2> {log.stderr}"
rule prepare_anvi_import_cat_taxonomy:
input:
report="logs/anvi-script-reformat-fasta_{assemblytype}_{hostcode}_{assemblyfile}.report",
taxonomy="data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}_taxonomy.tab",
profile=ancient("data/assembly_{assemblytype}_binningsignals_anvio/MERGED_{hostcode}/PROFILE.db")
output:
"data/assembly_{assemblytype}/{hostcode}/CAT_{hostcode}_{assemblyfile}_taxonomy_shortnames.tab"
threads: 2
conda:
"envs/anvio.yaml"
log:
"logs/prepare-anvi-import-cat-taxonomy_{assemblytype}_{hostcode}_{assemblyfile}.stderr"
shell:
"""
echo "item_name\tcategorical_kingdom\tcategorical_phylum\tcategorical_class\tcategorical_order\tcategorical_family\tcategorical_genus\tcategorical_species" \
> {output} 2> {log}
join -1 2 -2 1 \
<( sort -k2d {input.report} ) \
<(tail -n +2 {input.taxonomy} \
| cut -f 1,7- \
| sed 's/: [01]\.[0-9][0-9]//g' \
| tr ' ' '_' \
| sort -k1d )\
| tr ' ' '\t' \
| cut -f 2- \
| sort -n \
>> {output}.tmp 2>> {log}
join -1 1 -2 1 --check-order -a 1 \
<(anvi-get-split-coverages --list-splits -p {input.profile} \
2>> {log} \
| sed 's/_split/\t_split/g' | sort -k1d) \
<( sort -k1d {output}.tmp ) \
| tr ' ' '\t' \
| sort -k1n,2n \
| sed 's/\t_split/_split/g' \
>> {output} 2>> {log}
rm {output}.tmp 2>> {log}
"""