From aaf097a453233ded6b0ae2d3cdae71fbe801a678 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 9 Dec 2019 16:58:39 +0100
Subject: [PATCH] Using more processors to map and index.
Hopefully this will be more efficient on pisa.
---
CLIP/iCLIP.snakefile | 4 ++--
Degradome-seq/Degradome-seq.snakefile | 2 +-
PRO-seq/PRO-seq.snakefile | 8 +++++---
RNA_Seq_Cecere/RNA-seq.snakefile | 4 ++--
Ribo-seq/Ribo-seq.snakefile | 4 ++--
small_RNA-seq/small_RNA-seq.snakefile | 6 +++---
6 files changed, 15 insertions(+), 13 deletions(-)
diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile
index b52fb5f..69f346f 100644
--- a/CLIP/iCLIP.snakefile
+++ b/CLIP/iCLIP.snakefile
@@ -233,7 +233,7 @@ rule trim_and_dedup:
process_type = "iCLIP",
trim5 = 8,
trim3 = 4,
- threads: 4 # Actually, to avoid too much IO
+ threads: 8 # Actually, to avoid too much IO
message:
"Trimming adaptor from raw data using {wildcards.trimmer}, deduplicating reads, and removing 5' and 3' random n-mers for {wildcards.lib}_{wildcards.rep}."
benchmark:
@@ -470,7 +470,7 @@ rule sam2indexedbam:
log = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
threads:
- 4
+ 8
resources:
mem_mb=4100
wrapper:
diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile
index 91effc6..1628527 100644
--- a/Degradome-seq/Degradome-seq.snakefile
+++ b/Degradome-seq/Degradome-seq.snakefile
@@ -168,7 +168,7 @@ rule map_on_genome:
resources:
io=5
threads:
- 4
+ 8
wrapper:
f"file://{wrappers_dir}/map_on_genome"
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index bca5c25..7509054 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -392,7 +392,7 @@ rule trim_and_dedup:
process_type = "PRO-seq",
trim5 = lambda wildcards : lib2UMI[wildcards.lib][0],
trim3 = lambda wildcards : lib2UMI[wildcards.lib][1],
- threads: 4 # Actually, to avoid too much IO
+ threads: 8 # Actually, to avoid too much IO
message:
"Trimming adaptor from raw data using {wildcards.trimmer}, deduplicating reads, and removing 5' and 3' random n-mers for {wildcards.lib}_{wildcards.rep}."
benchmark:
@@ -429,7 +429,7 @@ rule trim_only:
process_type = "PRO-seq",
trim5 = lambda wildcards : lib2UMI[wildcards.lib][0],
trim3 = lambda wildcards : lib2UMI[wildcards.lib][1],
- threads: 4 # Actually, to avoid too much IO
+ threads: 8 # Actually, to avoid too much IO
message:
"Trimming adaptor from raw data using {wildcards.trimmer} and removing 5' and 3' random n-mers for {wildcards.lib}_{wildcards.rep}."
benchmark:
@@ -481,6 +481,8 @@ rule map_on_genome:
log:
log = OPJ(log_dir, "{trimmer}", "map_{type}_on_genome", "{lib}_{rep}.log"),
err = OPJ(log_dir, "{trimmer}", "map_{type}_on_genome", "{lib}_{rep}.err"),
+ threads:
+ 8
# shell:
# """
# genome_dir="${{HOME}}/Genomes"
@@ -506,7 +508,7 @@ rule sam2indexedbam:
log = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{type}.log"),
err = OPJ(log_dir, "{trimmer}", "sam2indexedbam", "{lib}_{rep}_{type}.err"),
threads:
- 4
+ 8
resources:
mem_mb=4100
wrapper:
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 9947973..1bb65ee 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -567,7 +567,7 @@ rule map_on_genome:
resources:
io=5
threads:
- 4
+ 8
#shell:
# mapping_command(aligner)
wrapper:
@@ -620,7 +620,7 @@ rule remap_on_genome:
resources:
io=5
threads:
- 4
+ 8
#shell:
# mapping_command(aligner)
wrapper:
diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile
index 5de9f9c..2afb5d9 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/Ribo-seq/Ribo-seq.snakefile
@@ -755,7 +755,7 @@ rule map_on_genome:
log = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_{read_type}.err")
threads:
- 4
+ 8
wrapper:
f"file://{wrappers_dir}/map_on_genome"
@@ -787,7 +787,7 @@ rule sam2indexedbam:
log = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
threads:
- 4
+ 8
resources:
mem_mb=4100
wrapper:
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index f287f44..c4616e3 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -1014,7 +1014,7 @@ rule map_on_genome:
log = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_%s.log" % size_selected),
err = OPJ(log_dir, "map_on_genome", "{lib}_{rep}_%s.err" % size_selected)
threads:
- 4
+ 8
resources:
mem_mb=700
wrapper:
@@ -1067,7 +1067,7 @@ rule remap_on_genome:
log = OPJ(log_dir, "remap_on_genome", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "remap_on_genome", "{lib}_{rep}_{read_type}.err")
threads:
- 4
+ 8
resources:
mem_mb=700
wrapper:
@@ -1102,7 +1102,7 @@ rule sam2indexedbam:
log = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.log"),
err = OPJ(log_dir, "sam2indexedbam", "{lib}_{rep}_{read_type}.err"),
threads:
- 4
+ 8
resources:
mem_mb=4100
wrapper:
--
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