Massive amount of files

[blediro]

Hey Jean-Sébastien,

I noticed that OPERA-MS generates a massive number of intermediate files (~250,000 per sample) when using the reference-based clustering option. This has become an issue when assembling multiple samples on the HPC, as it quickly exceeds my file quota (1,500,000).

Do you have any suggestions on how to manage this?

Best,
Juan

[jsgounot]

Hi Blediro,

sadly I'm not aware of a way to alleviate this issue right now. We're currently working on cleaning the OPERA-MS code and trying to fix this kind of thing, but this will not be done soon. Would you mind sharing what kind of samples you're working with? We usually see this kind of issue with samples with high coverage and high bacterial diversity, such as soil.

Regards,
JS

[blediro]

Hi JS,

I'm working with sludge samples from anaerobic digesters.

Best,

Juan