Feature request: checkpointing for fas.doAnno

[bheimbu]

Dear @trvinh,

it's me again, Bastian. I'm trying to get some proteomes annotated with fas.doAnno but our cluster walltime is set to 4 days and some proteomes are just too big -- even though I'm using 96 cores.

Would it be possible to implement checkpointing so an interrupted job can be re-started?

Cheers Bastian

[trvinh]

Hi Bastian,

currently it is not possible, because fas.doAnno stores the annotated features in memory until it writes the final JSON output. However I can create a script that can merge multiple JSON output files. This will allow you to split large proteomes into several smaller batches, run fas.doAnno on each one, and combine the results afterward.

I will let you know as soon as the merging script is ready.

Best,
Vinh

[bheimbu]

Hi, that sounds awesome. Looking forward to. Cheers and have a nice weekend, Bastian

…

Sent from my iPhone On 5. Dec 2025, at 13:46, Vinh Tran ***@***.***> wrote:  [https://avatars.githubusercontent.com/u/19269760?s=20&v=4]trvinh left a comment (BIONF/FAS#29)<#29 (comment)> Hi Bastian, currently it is not possible, because fas.doAnno stores the annotated features in memory until it writes the final JSON output. However I can create a script that can merge multiple JSON output files. This will allow you to split large proteomes into several smaller batches, run fas.doAnno on each one, and combine the results afterward. I will let you know as soon as the merging script is ready. Best, Vinh — Reply to this email directly, view it on GitHub<#29 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AF67TI6T7F3SFKX3WQXQO6D4AF5DLAVCNFSM6AAAAACOD67TSGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMMJWG44TSNJVGQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[trvinh]

Hi Bastian,

please try the new version and use the function fas.mergeAnno to merge the annotation json files. To use it, place all json files that need to be combined into a single folder, then run

fas.mergeAnno -i /path/to/that/folder -o <output_file.json>

Please let me know if it works!

Have a nice weekend!
Vinh

[bheimbu]

Hi @trvinh,

that works perfectly. Many thanks.

Cheers Bastian