fix vardict memory error

Clinical-Genomics · Oct 21, 2024 · fe210bf · fe210bf
1 parent 061c4bb
commit fe210bf
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Showing 3 changed files with 5 additions and 2 deletions.
diff --git a/BALSAMIC/snakemake_rules/variant_calling/snv_t_varcall_tga.rule b/BALSAMIC/snakemake_rules/variant_calling/snv_t_varcall_tga.rule
@@ -93,7 +93,8 @@ rule vardict_tumor_only:
 export PERL5LIB=;
 
 export TMPDIR={params.tmpdir};
-export VAR_DICT_OPTS='\"-Djava.io.tmpdir={params.tmpdir}\" \"-Xmx45G\"'; 
+export _JAVA_OPTIONS="-Djava.io.tmpdir={params.tmpdir}"; 
+export VAR_DICT_OPTS='\"-Xms45G\" \"-Xmx90G\"'; 
 
 vardict-java -I 600 \
 -G {input.fa} \

diff --git a/BALSAMIC/snakemake_rules/variant_calling/snv_tn_varcall_tga.rule b/BALSAMIC/snakemake_rules/variant_calling/snv_tn_varcall_tga.rule
@@ -94,7 +94,8 @@ rule vardict_tumor_normal:
     shell:
         """
 export TMPDIR={params.tmpdir};
-export VAR_DICT_OPTS='\"-Djava.io.tmpdir={params.tmpdir}\" \"-Xmx90G\"';
+export _JAVA_OPTIONS="-Djava.io.tmpdir={params.tmpdir}"; 
+export VAR_DICT_OPTS='\"-Xms45G\" \"-Xmx90G\"'; 
 
 vardict-java -I 600 -G {input.fa} -f {params.af} -N {params.case_name} \
 -b \"{input.bamT}|{input.bamN}\" \

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -58,6 +58,7 @@ Fixed:
 * CNVkit incorrect version in the documentation https://github.com/Clinical-Genomics/BALSAMIC/pull/1457
 * MSIsensor-pro container and updated msisensor to version 1.3.0  https://github.com/Clinical-Genomics/BALSAMIC/pull/1486
 * Somalier container and updated somalier to version 0.2.19 https://github.com/Clinical-Genomics/BALSAMIC/pull/1487
+* Vardict memory and tmpdir allocation https://github.com/Clinical-Genomics/BALSAMIC/pull/
 
 [15.0.1]
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