Update: java Xmx32g

tasks/Pindel.wdl

@@ -25,7 +25,7 @@ task Pindel {
     
     samtools index -@ 4 ./input/$bam_file_name
     
-    java "-Xmx16G" -jar /software/picard/picard.jar CollectInsertSizeMetrics \
+    java "-Xmx32G" -jar /software/picard/picard.jar CollectInsertSizeMetrics \
       -H ./pindel_result/${sample_id}_picard.pdf \
       -I ./input/$bam_file_name \
       -O ./pindel_result/${sample_id}_picard.txt

tasks/processSomatic.wdl

@@ -11,8 +11,8 @@ task processSomatic {
   command <<<
     cp ${varscan_snp} ./
     cp ${varscan_indel} ./
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.SNP.vcf
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.INDEL.vcf
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.SNP.vcf
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar processSomatic ${sample}.VarScan.INDEL.vcf
 
   >>>
 

tasks/somatic.wdl

@@ -13,7 +13,7 @@ task somatic {
   String disk_size
 
   command <<<
-    samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.SNP --output-indel ${sample}.VarScan.INDEL --strand-filter 1
+    samtools mpileup -f ${ref_dir}/${fasta} -B ${normal_bam} ${tumor_bam} | java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somatic --mpileup 1 --min-coverage 3 --min-coverage-normal 3 --min-coverage-tumor 3 --min-var-freq 0.08 --p-value 0.10 --somatic-p-value 0.05 --output-vcf 1 --output-snp ${sample}.VarScan.SNP --output-indel ${sample}.VarScan.INDEL --strand-filter 1
   >>>
 
   runtime {

tasks/somaticFilter.wdl

@@ -14,17 +14,17 @@ task somaticFilter {
   String disk_size
 
   command <<<
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Somatic.filter.vcf
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Somatic.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Germline.filter.vcf
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.Germline.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.LOH.filter.vcf
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_snp_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --indel-file ${varscan_indel} --output-file ${sample}.VarScan.SNP.LOH.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Somatic.filter.vcf
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_somatic_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Somatic.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Germline.filter.vcf
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_germline_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.Germline.filter.vcf
 
-    java -Xmx16g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.LOH.filter.vcf
+    java -Xmx32g -jar /opt/VarScan.v2.4.3.jar somaticFilter ${varscan_indel_loh_hc} --min-coverage 10 --min-reads2 2 --min-strands2 1 --min-avg-qual 20 --p-value 0.1 --output-file ${sample}.VarScan.INDEL.LOH.filter.vcf
 
     # Merge SNP and INDEL
     awk '{if ($1!~/^#/) print}' ${sample}.VarScan.SNP.Somatic.filter.vcf | cat ${sample}.VarScan.INDEL.Somatic.filter.vcf - > ${sample}.VarScan.Somatic.filter.vcf