Dorado correct killed without explanation

[JasonJWilliamsNY]

Issue Report

Please describe the issue:

Please provide a clear and concise description of the issue you are seeing and the result you expect.

I run 'dorado correct -v filtered_simplex_reads.fastq >output.fasta' this seems to run well for a few hours and then is killed. Without any used debug or error message about ~20% in.

Steps to reproduce the issue:

Please list any steps to reproduce the issue.

As above.

Run environment:

• Dorado version: 0.7.2
• Dorado command: correct
• Operating system: Ubuntu 20.04.6 LTS
• Hardware (CPUs, Memory, GPUs): 32 CPU, 125 GB RAM, 1vGPU —NVIDIA A100 SXM4 40GB
• Source data type (e.g., pod5 or fast5 - please note we always recommend converting to pod5 for optimal basecalling performance): fastq
• Source data location (on device or networked drive - NFS, etc.): Network drive
• Details about data (flow cell, kit, read lengths, number of reads, total dataset size in MB/GB/TB): 112GB fastq input
• Dataset to reproduce, if applicable (small subset of data to share as a pod5 to reproduce the issue):

Logs

• Please provide output trace of dorado (run dorado with -v, or -vv on a small subset). I can't find any logs

[malton-ont]

Hi @JasonJWilliamsNY,

I suspect you are running out of memory. From the dorado correct documentation:

The error correction tool is both compute and memory intensive. As a result, it is best run on a system with multiple high performance CPU cores ( > 64 cores), large system memory ( > 256GB) and a modern GPU with a large VRAM ( > 32GB).

[JasonJWilliamsNY]

Thanks. I did get this to run on a much larger system. Without any specific memory error I couldn't be sure what happened.