Snakemake Report

Loading Snakemake Report...

Please enable Javascript in your browser to see this report.

Loading 15.7 MB. For large reports, this can take a while.

Workflow

Click the nodes to obtain details about each step.

figures

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

File Code

sample: small
fasta: .test/small.fasta
window: 1000 
nbatch: 4 
alnthreads: 4 
mm_f: 10000 
tempdir: temp

Jobs 1

Input files

results/{SM}.{W}.{F}.bed.gz

Output files

results/{SM,arabidopsis}.{W,1000}.{F,10000}_figures/pdfs/{SM}.{W}.{F}.tri.TRUE__onecolorscale.FALSE__all.pdf
results/{SM,arabidopsis}.{W,1000}.{F,10000}_figures/pngs/{SM}.{W}.{F}.tri.TRUE__onecolorscale.TRUE__all.png
results/{SM,arabidopsis}.{W,1000}.{F,10000}_figures/pngs/{SM}.{W}.{F}.tri.TRUE__onecolorscale.FALSE__all.png
results/{SM,arabidopsis}.{W,1000}.{F,10000}_figures/pngs/{SM}.{W}.{F}.tri.FALSE__onecolorscale.TRUE__all.png
results/{SM,arabidopsis}.{W,1000}.{F,10000}_figures/pngs/{SM}.{W}.{F}.tri.FALSE__onecolorscale.FALSE__all.png
results/{SM,arabidopsis}.{W,1000}.{F,10000}_figures/pngs/{SM}.{W}.{F}.facet.all.png

Conda software stack

xorg-libx11
xorg-libxau
r-base>=4.0
r-essentials
r-cairo
r::r-tidyverse
r-data.table
r-cowplot
r-argparse
r-glue
r::r-rcolorbrewer
r::r-scales
r::r-ggplot2
r-r.utils

Code

1 2	`Rscript {params.sdir}/scripts/aln_plot.R --bed {input.bed} --threads {threads} --prefix {wildcards.SM}.{wildcards.W}.{wildcards.F}`

Jobs 1

Input files

temp/{SM}.{W}.{F}.tbl.gz
/Users/mrvollger/Desktop/repos/StainedGlass/Col-CEN_v1.2.fasta.fai

Output files

results/{SM,arabidopsis}.{W,1000}.{F,10000}.bed.gz
results/{SM,arabidopsis}.{W,1000}.{F,10000}.full.tbl.gz

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`{params.sdir}/scripts/refmt.py --window {wildcards.W} --fai {input.fai} --full {output.full} {params.one} {input.tbl} {output.bed}`

Jobs 1

Input files

results/{SM}.{W}.{F}.sorted.bam

Output files

temp/{SM,arabidopsis}.{W,1000}.{F,10000}.tbl.gz

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`{params.sdir}/scripts/samIdentity.py --threads {threads} --matches {params.S} --header {input.aln} \| pigz -p {threads} > {output.tbl}`

Jobs 1

Input files

temp/{SM}.{W}.{F}.bam

Output files

results/{SM,arabidopsis}.{W,1000}.{F,10000}.sorted.bam

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`samtools sort -m {resources.mem}G -@ {threads} --write-index -o {output.aln} {input.aln}`

Jobs 1

Input files

temp/{SM}.{W}.{F}.list
temp/{SM}.{W}.{F}.0.bam
temp/{SM}.{W}.{F}.1.bam
temp/{SM}.{W}.{F}.2.bam
temp/{SM}.{W}.{F}.3.bam
results/{SM}.{W}.fasta

Output files

temp/{SM,arabidopsis}.{W,1000}.{F,10000}.bam

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`samtools cat -b {input.alns} -o {output.aln}`

Rule properties
Input files
Jobs	1
temp/{SM}.{W}.{F}.0.bam temp/{SM}.{W}.{F}.1.bam temp/{SM}.{W}.{F}.2.bam temp/{SM}.{W}.{F}.3.bam
Output files
temp/{SM,arabidopsis}.{W,1000}.{F,10000}.list

Jobs 4

Input files

/Users/mrvollger/Desktop/repos/StainedGlass/Col-CEN_v1.2.fasta
temp/{SM}.{W}.{ID}.bed
temp/{SM}.{W}.{F}.fasta.mmi

Output files

temp/{SM,arabidopsis}.{W,1000}.{F,10000}.{ID,0|1|2|3}.bam

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1
2

        ( minimap2             -t {threads}             -f {wildcards.F} -s {params.S}             {params.MAP_PARAMS}             --dual=yes --eqx             {input.split_ref}             <( bedtools getfasta -fi {input.ref} -bed {input.bed} )             | samtools sort -m {resources.mem}G             -o {output.aln}         ) 2> {log}

Jobs 1

Input files

temp/{SM}.{W}.bed

Output files

temp/{SM,arabidopsis}.{W,1000}.0.bed
temp/{SM,arabidopsis}.{W,1000}.1.bed
temp/{SM,arabidopsis}.{W,1000}.2.bed
temp/{SM,arabidopsis}.{W,1000}.3.bed

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`{params.sdir}/scripts/batch_bed_files.py {input.bed} --outputs {output.bed}`

Jobs 1

Input files

/Users/mrvollger/Desktop/repos/StainedGlass/Col-CEN_v1.2.fasta.fai

Output files

temp/{SM,arabidopsis}.{W,1000}.bed

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`bedtools makewindows -g {input.fai} -w {wildcards.W} {params.slide} > {output.bed}`

Jobs 1

Input files

results/{SM}.{W}.fasta

Output files

temp/{SM,arabidopsis}.{W,1000}.{F,10000}.fasta.mmi

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`minimap2 -f {wildcards.F} -s {params.S} {params.MAP_PARAMS} -d {output.split_ref_index} {input.ref} 2> {log}`

Jobs 1

Input files

/Users/mrvollger/Desktop/repos/StainedGlass/Col-CEN_v1.2.fasta
temp/{SM}.{W}.bed

Output files

results/{SM,arabidopsis}.{W,1000}.fasta

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`bedtools getfasta -fi {input.ref} -bed {input.bed} > {output.fasta}`

Jobs 1

Input files

results/{SM}.{W}.{F}.bed.gz
/Users/mrvollger/Desktop/repos/StainedGlass/Col-CEN_v1.2.fasta.fai

Output files

results/{SM,arabidopsis}.{W,1000}.{F,10000}.strand.cool

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1
2

        gunzip -c {input.bed} | tail -n +2             | sed  's/+$/100/g'             | sed  's/-$/50/g'               | cooler cload pairs                 -c1 1 -p1 2 -c2 4 -p2 5                         --field count=8:agg=mean,dtype=float                 --chunksize 50000000000                 {input.fai}:{wildcards.W}                 --zero-based                 - {output.cool}

Jobs 1

Input files

results/{SM}.{W}.{F}.bed.gz
/Users/mrvollger/Desktop/repos/StainedGlass/Col-CEN_v1.2.fasta.fai

Output files

results/{SM,arabidopsis}.{W,1000}.{F,10000}.identity.cool

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1
2
3

        gunzip -c {input.bed} | tail -n +2               | cooler cload pairs                 -c1 1 -p1 2 -c2 4 -p2 5                         --field count=7:agg=mean,dtype=float                 --chunksize 50000000000                 {input.fai}:{wildcards.W}                 --zero-based                 - {output.cool}

Jobs 1

Input files

results/{SM}.{W}.{F}.strand.cool

Output files

results/{SM,arabidopsis}.{W,1000}.{F,10000}.strand.mcool

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`cooler zoomify --field count:agg=mean,dtype=float {input.s} -n {threads} -o {output.s}`

Jobs 1

Input files

results/{SM}.{W}.{F}.identity.cool

Output files

results/{SM,arabidopsis}.{W,1000}.{F,10000}.identity.mcool

Conda software stack

pandas
numpy
numba
cooler
minimap2>=2.17.0
bedtools
samtools>=1.9
pysam
snakemake>=6.0
snakefmt
bwa
pigz

Code

1 2	`cooler zoomify --field count:agg=mean,dtype=float {input.i} -n {threads} -o {output.i}`