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RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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Continue stopped assembly job #15

Closed chezus666 closed 3 years ago

chezus666 commented 3 years ago

Hi all, thanks for the nice piece of software! I had an assembly running, which was stopped because I did not allocate enough memory. I used metaspades as assembler which has the option "--continue" to continue started jobs, and I was wondering if there is a way to tell Mitofinder to tell metaspades to use this option. Or generally how can I change parameters in the programs Mitofinder uses.

Cheers!

RemiAllio commented 3 years ago

Hi,

I didn't know that it was possible to continue a stopped assembly with metaSPAdes. So there is no option within MitoFinder for this (good point for the next version, thanks!). However, I think the easiest way to continue the stopped assembly is to use metaSPAdes separately and then give the resulted assembly to MitoFinder with the -a option.

So, you can use the metaspades.py of the MitoFinder repository: path/to/MitoFinder/metaspades/bin/metaspades.py with the specific options to continue the assembly. The output folder of metaSPAdes to specify for this option should be named [SeqID]_metaspades in the output folder of MitoFinder,

Once the assembly is completed, you can run MitoFinder again with the -a option by specifying the result of metaSPAdes as input assembly.

I hope this helps, Cheers, Rémi

chezus666 commented 3 years ago

Hi, okay thanks for the fast reply! I will try that.

Cheers!

RemiAllio commented 3 years ago

Hi,

Let me know if it works or if you have any problems.

Cheers, Rémi

chezus666 commented 3 years ago

Hi, I made some changes to the dataset, therefore I had to rerun it anyway, so I didnt try your suggestion after all. But generally I think it would be cool if there would be an easy option to adress the parameters of the assemblers Mitofinder uses. Cheers!

RemiAllio commented 3 years ago

Hi,

All right. I agree, I have to think about how to implement it for the next version of MitoFinder!

Thank you for your feedback,

Cheers, Rémi