Starting Call Set Refinement (CSR) filtering provokes RAM overload
amolares opened this issue · comments
Hi.
I'm trying to analyze data from viruses (in illumina paired end fastq format), with a size of 100 MB for the sum of R1 and R2, in a machine with 16 cores and 30 GB of ram memory.
In previous steps, fastp tool is used to filtering and trimming adapters from raw data, and bwa mem to generate aligned cram file.
When Starting Call Set Refinement (CSR) filtering section is reached, RAM is growing up to the 100% of load capacity and kill the process abruptly.
- Reference fasta and CRAM files may be downloaded from this link:
https://filesender.uvigo.es/?s=download&token=4bced40f-f8cd-4930-a373-fc68e59e7a64
Version
octopus version 0.7.4
Command
vhd.run.cloud.sh: line 82: 72876 Killed
$ octopus --threads $THREADS -P 1 -R $VIRUSREF -I $SAMPLE.CRAM --annotations AD ADP AF --sequence-error-model PCR-free.HiSeq-2500 -o $SAMPLE.OG.vcf.gz
Additional context
Previously, another sample of same type of virus, but with a size of 33 MB for the sum of R1 and R2 fastq files, was completely done, with no errors.
Thank you very much for your support.