OOM error for GetPileupSummaries on EC2 #2131
Description
Description of the bug
Dear developers:
I am running one pair of whole exome samples from TCGA on AWS instances. The instance is m4.16xlarge with 64 cpus and 256 GB. I am experiencing over 24 hrs on BWA and it failed at NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:GETPILEUPSUMMARIES_TUMOR (tumor_sample). Is there configuration error? Thank you.
Command used and terminal output
nextflow run nf-core/sarek -r 3.7.0 -profile conda \--input ./sample_sarek.csv --step mapping --outdir ./results \--aligner bwa-mem2 --genome GATK.GRCh38 \--tools mutect2,strelka -with-report --dbsnp ../database/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz --known_indels ../database/Homo_sapiens_assembly38.known_indels.vcf.gz --pon ../database/PON.sorted.vcf.gz --pon_tbi ../database/PON.sorted.vcf.gz.tbi --germline_resource ../database/af-only-gnomad.hg38.vcf.gz --wes --intervals ../database/GRCh38_exome.bed --only_paired_variant_calling --dbsnp_tbi ../database/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi --skip_tools baserecalibrator,baserecalibrator_report --no_intervalsRelevant files
No response
System information
No response