From 9b50863bc1f20158445a4164ef98250e19bcdfe9 Mon Sep 17 00:00:00 2001
From: tfaraut <Thomas.Faraut@inra.fr>
Date: Wed, 12 Dec 2018 16:55:59 +0100
Subject: [PATCH] - pindel back to --max_range_index 3 - gstrip_preprocess now
requires 16Gb of memory
---
cluster.yaml | 2 +-
snakecnv/bin/gstrip_preprocess.py | 4 ++--
snakecnv/tools/pindel.snk | 3 ++-
3 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/cluster.yaml b/cluster.yaml
index ebcfc93..43a7f96 100644
--- a/cluster.yaml
+++ b/cluster.yaml
@@ -18,7 +18,7 @@ genomestrip:
mem: 8
preprocess:
- mem: 8
+ mem: 16
time: "72:00:00"
cnvpipeline:
diff --git a/snakecnv/bin/gstrip_preprocess.py b/snakecnv/bin/gstrip_preprocess.py
index 5e12135..c65492e 100755
--- a/snakecnv/bin/gstrip_preprocess.py
+++ b/snakecnv/bin/gstrip_preprocess.py
@@ -40,7 +40,7 @@ def launch(bamlist, reference, gendermap, outdir, outprefix):
old_libpath = ":" + os.environ["LD_LIBRARY_PATH"] if "LD_LIBRARY_PATH" in os.environ else ""
os.environ["LD_LIBRARY_PATH"] = sv_dir + "/bwa" + old_libpath
- mx = "-Xmx4g"
+ mx = "-Xmx16g"
classpath = "{sv_dir}/lib/SVToolkit.jar:{sv_dir}/lib/gatk/GenomeAnalysisTK.jar:{sv_dir}/lib/gatk/Queue.jar". \
format(sv_dir=sv_dir)
@@ -58,7 +58,7 @@ def launch(bamlist, reference, gendermap, outdir, outprefix):
.format(classpath=classpath, mx=mx, sv_dir=sv_dir), shell=True).returncode
if exit_code != 0:
return fail("An error has occurred. See above.")
-
+
command = (
"""LC_ALL=C java -cp {classpath} {mx} \
org.broadinstitute.gatk.queue.QCommandLine \
diff --git a/snakecnv/tools/pindel.snk b/snakecnv/tools/pindel.snk
index d290f74..acb74cd 100644
--- a/snakecnv/tools/pindel.snk
+++ b/snakecnv/tools/pindel.snk
@@ -41,10 +41,11 @@ rule pindel:
shell:
"pindel -f {input.genome} -i {input.statfile}"
" --min_perfect_match_around_BP 20 "
+ " --max_range_index 3 "
" --exclude {input.excluded}"
" --number_of_threads {threads}"
" --report_interchromosomal_events false"
- " --window_size 1" # 1Mb
+ " --window_size 1" # 1Mb
" --minimum_support_for_event 3 -c {wildcards.chrom}:{wildcards.chrbatch}"
" -o {wildcards.batch}/pindel/{wildcards.chrom}/{wildcards.chrbatch}/pindel_{wildcards.chrom}"
" 1>{log.stdout} 2>{log.stderr}"
--
GitLab