I've followed your vignette and get to the point of running readsToTarget with 27 bam files (they are quite large - 80 - 120GB) based on paired samples. I'm running on a Amazon Linux 2 EC2 w/32 cores and ~128 GB RAM. I can see in top that the function progressively increases RAM usage to the point where it eventually kills R. I even tried it with just a single BAM file and same result.
Do you have any suggestions for a multi-threading option? Or have you experienced this with large BAM files? Any other suggestions?
I've followed your vignette and get to the point of running readsToTarget with 27 bam files (they are quite large - 80 - 120GB) based on paired samples. I'm running on a Amazon Linux 2 EC2 w/32 cores and ~128 GB RAM. I can see in top that the function progressively increases RAM usage to the point where it eventually kills R. I even tried it with just a single BAM file and same result.
Do you have any suggestions for a multi-threading option? Or have you experienced this with large BAM files? Any other suggestions?
Thank you!