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@ksahlin
ksahlin committed Apr 28, 2021
1 parent e5e082a commit 3bb19b7
Showing 1 changed file with 15 additions and 15 deletions.
30 changes: 15 additions & 15 deletions evaluation/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -184,9 +184,9 @@ rule ultra_align:
ultra_src = config["uLTRA_src"]
outfolder = config["ROOT_OUT"] + "/alignments/ultra/{0}/".format(wildcards.dataset)
if wildcards.dataset == 'pacbio_alzheimer' or wildcards.dataset == "simulated_ens":
shell("/usr/bin/time -v {ultra_src}/uLTRA align {ref} {input.reads} {outfolder} --min_mem 20 --min_acc 0.8 --t 19 --disable_mm2 2>&1 | tee {output.time_and_mem} ") # 2> {output.time_and_mem}
shell("/usr/bin/time -v {ultra_src}/uLTRA align {ref} {input.reads} {outfolder} --min_mem 20 --min_acc 0.8 --t 4 --disable_mm2 2>&1 | tee {output.time_and_mem} ") # 2> {output.time_and_mem}
else:
shell("/usr/bin/time -v {ultra_src}/uLTRA align {ref} {input.reads} {outfolder} --min_mem 17 --min_acc 0.6 --t 19 --disable_mm2 2>&1 | tee {output.time_and_mem} ") # 2> {output.time_and_mem}
shell("/usr/bin/time -v {ultra_src}/uLTRA align {ref} {input.reads} {outfolder} --min_mem 17 --min_acc 0.6 --t 4 --disable_mm2 2>&1 | tee {output.time_and_mem} ") # 2> {output.time_and_mem}

# shell("mv {outfolder}/torkel.sam {output.sam}")

Expand Down Expand Up @@ -242,9 +242,9 @@ rule ultra_mm2_align:
ultra_src = config["uLTRA_src"]
outfolder = config["ROOT_OUT"] + "/alignments/ultra_mm2/{0}/".format(wildcards.dataset)
if wildcards.dataset == 'pacbio_alzheimer' or wildcards.dataset == "simulated_ens":
shell("/usr/bin/time -v {ultra_src}/uLTRA align {ref} {input.reads} {outfolder} --min_mem 20 --min_acc 0.8 --t 19 2>&1 | tee {output.time_and_mem} ") # 2> {output.time_and_mem}
shell("/usr/bin/time -v {ultra_src}/uLTRA align {ref} {input.reads} {outfolder} --min_mem 20 --min_acc 0.8 --t 4 2>&1 | tee {output.time_and_mem} ") # 2> {output.time_and_mem}
else:
shell("/usr/bin/time -v {ultra_src}/uLTRA align {ref} {input.reads} {outfolder} --min_mem 17 --min_acc 0.6 --t 19 2>&1 | tee {output.time_and_mem} ") # 2> {output.time_and_mem}
shell("/usr/bin/time -v {ultra_src}/uLTRA align {ref} {input.reads} {outfolder} --min_mem 17 --min_acc 0.6 --t 4 2>&1 | tee {output.time_and_mem} ") # 2> {output.time_and_mem}

# shell("mv {outfolder}/torkel.sam {output.sam}")

Expand Down Expand Up @@ -283,11 +283,11 @@ rule minimap2_align:
run:

if wildcards.dataset == "sirv":
shell("/usr/bin/time -v minimap2 --eqx -t 19 -ax splice -k13 --splice-flank=no --secondary=no -C5 {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
shell("/usr/bin/time -v minimap2 --eqx -t 4 -ax splice -k13 --splice-flank=no --secondary=no -C5 {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
elif wildcards.dataset == "pacbio_alzheimer" :
shell("/usr/bin/time -v minimap2 --eqx -t 19 -ax splice -k14 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
shell("/usr/bin/time -v minimap2 --eqx -t 4 -ax splice -k14 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
else:
shell("/usr/bin/time -v minimap2 --eqx -t 19 -ax splice -k13 -w 5 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
shell("/usr/bin/time -v minimap2 --eqx -t 4 -ax splice -k13 -w 5 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")



Expand All @@ -300,16 +300,16 @@ rule minimap2_gtf_align:

if wildcards.dataset == "sirv":
annotation = config["ANNOTATION"] + "/SIRV.bed"
shell("/usr/bin/time -v minimap2 --junc-bed {annotation} --eqx -t 19 -ax splice -k13 --splice-flank=no {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
shell("/usr/bin/time -v minimap2 --junc-bed {annotation} --eqx -t 4 -ax splice -k13 --splice-flank=no {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
elif wildcards.dataset == "drosophila":
annotation = config["ANNOTATION"] + "/drosophila.bed"
shell("/usr/bin/time -v minimap2 --junc-bed {annotation} --eqx -t 19 -ax splice -k13 -w 5 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
shell("/usr/bin/time -v minimap2 --junc-bed {annotation} --eqx -t 4 -ax splice -k13 -w 5 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
elif wildcards.dataset == "pacbio_alzheimer" :
annotation = config["ANNOTATION"] + "/NA12878.bed"
shell("/usr/bin/time -v minimap2 --junc-bed {annotation} --eqx -t 19 -ax splice -k14 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
shell("/usr/bin/time -v minimap2 --junc-bed {annotation} --eqx -t 4 -ax splice -k14 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
else:
annotation = config["ANNOTATION"] + "/NA12878.bed"
shell("/usr/bin/time -v minimap2 --junc-bed {annotation} --eqx -t 19 -ax splice -k13 -w 5 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")
shell("/usr/bin/time -v minimap2 --junc-bed {annotation} --eqx -t 4 -ax splice -k13 -w 5 -G 500k {input.index} {input.fastq} 1> {output.sam} 2> {output.time_and_mem} ")



Expand Down Expand Up @@ -368,9 +368,9 @@ rule desalt_align:
work_dir = tempfile.mkdtemp()
tempfile = os.path.join(work_dir, "desalt_temp_prefix")
if wildcards.dataset == "sirv":
shell("/usr/bin/time -v deSALT aln {index} {input.fastq} --noncan 4 -d 10 -s 2 -l 14 -t 19 -o {output.sam} -f {tempfile} 2>&1 | tee {output.time_and_mem} ")
shell("/usr/bin/time -v deSALT aln {index} {input.fastq} --noncan 4 -d 10 -s 2 -l 14 -t 4 -o {output.sam} -f {tempfile} 2>&1 | tee {output.time_and_mem} ")
else:
shell("/usr/bin/time -v deSALT aln {index} {input.fastq} --max-intron-len 500000 -d 10 -s 2 -l 14 -t 19 -o {output.sam} -f {tempfile} 2>&1 | tee {output.time_and_mem} ")
shell("/usr/bin/time -v deSALT aln {index} {input.fastq} --max-intron-len 500000 -d 10 -s 2 -l 14 -t 4 -o {output.sam} -f {tempfile} 2>&1 | tee {output.time_and_mem} ")


rule desalt_gtf_align:
Expand All @@ -387,10 +387,10 @@ rule desalt_gtf_align:
work_dir = tempfile.mkdtemp()
tempfile = os.path.join(work_dir, "desalt_gtf_temp_prefix")
if wildcards.dataset == "sirv":
shell("/usr/bin/time -v deSALT aln {index} {input.fastq} --noncan 4 -d 10 -s 2 -l 14 -t 19 --gtf {input.desalt_gtf_annotation_outfile} -o {output.sam} -f {tempfile} 2>&1 | tee {output.time_and_mem} ")
shell("/usr/bin/time -v deSALT aln {index} {input.fastq} --noncan 4 -d 10 -s 2 -l 14 -t 4 --gtf {input.desalt_gtf_annotation_outfile} -o {output.sam} -f {tempfile} 2>&1 | tee {output.time_and_mem} ")
else:
# Switch back to deSALT-1.5.5 on ALZ because newer version segfaults
shell("/usr/bin/time -v deSALT-1.5.5 aln {index} {input.fastq} --max-intron-len 500000 -d 10 -s 2 -l 14 -t 19 --gtf {input.desalt_gtf_annotation_outfile} -o {output.sam} -f {tempfile} 2>&1 | tee {output.time_and_mem} ")
shell("/usr/bin/time -v deSALT-1.5.5 aln {index} {input.fastq} --max-intron-len 500000 -d 10 -s 2 -l 14 -t 4 --gtf {input.desalt_gtf_annotation_outfile} -o {output.sam} -f {tempfile} 2>&1 | tee {output.time_and_mem} ")


# rule graphmap2_index:
Expand Down

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