Out of Memory

[jiaolaboratory]

Out of Memory

[JiaoLaboratory]

This situation is possible, but based on our tests, it occurs almost exclusively in the case of exceptionally long single chromosomes (e.g., when the length of a single chromosome exceeds 300 Mb). Generally, CRAQ consumes more memory when processing high-noise ONT data compared to HiFi data. Even although the memory usage still remains within manageable limits. By the way, could you please provide information on how your 'lgs.sort.bam' was generated? Additionally, if the memory issue cannot be resolved, based on our experience, reducing the usage of long reads (e.g., using only 50X coverage ) is almost no impact on the final results.

[yangfangyuan0102]

Hi, @JiaoLaboratory
Thank you for your reply. I mapped the long reads using minimap2 with typical options "-ax map-pb | samtools view -F1796 -q 20 | samtools sort ....". I tried to reduce datasize in half, 75X. Memory is still insufficient.
One thing I realized was that my genome was polished by long- and short-reads mutiple time, so it could be very different from the raw long reads. Will this cause the raw long reads to be too noisy?

[JiaoLaboratory]

It's highly likely that this is the cause. Currently, CRAQ's handling of high-noise alignments consumes significant resources. Would you mind trying the previous version of CRAQ-v1.0.8 (https://github.com/JiaoLaboratory/CRAQ/releases/download/v1.0.8/CRAQ-v1.0.8.zip)? This version lacks optimizations for high-accuracy data processing (which consumes resources in that step), but there haven't been significant changes in handling high-noise ONT/CRL data with CRAQ-v1.0.9.

[yangfangyuan0102]

It's highly likely that this is the cause. Currently, CRAQ's handling of high-noise alignments consumes significant resources. Would you mind trying the previous version of CRAQ-v1.0.8 (https://github.com/JiaoLaboratory/CRAQ/releases/download/v1.0.8/CRAQ-v1.0.8.zip)? This version lacks optimizations for high-accuracy data processing (which consumes resources in that step), but there haven't been significant changes in handling high-noise ONT/CRL data with CRAQ-v1.0.9.

Great, The version 1.0.8 works. Thank you!