fix: give melt more memory

bihealth · Feb 9, 2023 · 2da20ce · 2da20ce
1 parent 65c5b6e
commit 2da20ce
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Showing 6 changed files with 6 additions and 6 deletions.
diff --git a/snappy_pipeline/workflows/common/melt.py b/snappy_pipeline/workflows/common/melt.py
@@ -43,7 +43,7 @@ class MeltStepPart(
     _resource_usage = ResourceUsage(
         threads=1,
         time="1-00:00:00",
-        memory="6G",
+        memory="12G",
     )
     resource_usage_dict = {
         "preprocess": _resource_usage,

diff --git a/snappy_wrappers/wrappers/melt/genotype/wrapper.py b/snappy_wrappers/wrappers/melt/genotype/wrapper.py
@@ -16,7 +16,7 @@
 ME_REFS={melt_config[me_refs_path]}
 ME_INFIX={melt_config[me_refs_infix]}
 
-java -Xmx6G -jar $JAR \
+java -Xmx8G -jar $JAR \
     Genotype \
     -h {snakemake.config[static_data_config][reference][path]} \
     -bamfile {snakemake.input.bam} \

diff --git a/snappy_wrappers/wrappers/melt/group_analysis/wrapper.py b/snappy_wrappers/wrappers/melt/group_analysis/wrapper.py
@@ -16,7 +16,7 @@
 ME_REFS={melt_config[me_refs_path]}
 ME_INFIX={melt_config[me_refs_infix]}
 
-java -jar -Xmx6G -jar $JAR \
+java -jar -Xmx8G -jar $JAR \
     GroupAnalysis \
     -h {snakemake.config[static_data_config][reference][path]} \
     -t $ME_REFS/$ME_INFIX/{snakemake.wildcards.me_type}_MELT.zip \

diff --git a/snappy_wrappers/wrappers/melt/indiv_analysis/wrapper.py b/snappy_wrappers/wrappers/melt/indiv_analysis/wrapper.py
@@ -17,7 +17,7 @@
 ME_REFS={melt_config[me_refs_path]}
 ME_INFIX={melt_config[me_refs_infix]}
 
-java -Xmx6G -jar $JAR \
+java -Xmx8G -jar $JAR \
     IndivAnalysis \
     -b hs37d5/NC_007605 \
     {melt_arg_exome} \

diff --git a/snappy_wrappers/wrappers/melt/make_vcf/wrapper.py b/snappy_wrappers/wrappers/melt/make_vcf/wrapper.py
@@ -22,7 +22,7 @@
 > {snakemake.output.list_txt}
 
 # TODO: allowing 100% no-call wise?
-java -Xmx6G -jar $JAR \
+java -Xmx8G -jar $JAR \
     MakeVCF \
     -genotypingdir $genotype_dir \
     -h {snakemake.config[static_data_config][reference][path]} \

diff --git a/snappy_wrappers/wrappers/melt/preprocess/wrapper.py b/snappy_wrappers/wrappers/melt/preprocess/wrapper.py
@@ -17,7 +17,7 @@
 
 JAR={melt_config[jar_file]}
 
-java -Xmx4G -jar $JAR \
+java -Xmx8G -jar $JAR \
     Preprocess \
     -bamfile {snakemake.output.orig_bam} \
     -h {snakemake.config[static_data_config][reference][path]}