Gold standard assembly and binning ran despite being set to false

[elximo]

Hi CAMISIM,

Thanks for the great tool. I have just started to use it to generate metagenomes based on a custom profile. Since I am using genomes of assemblies of relatively new strains, I am using the metagenomesimulation.py my_config.ini

To save time and since I am not interested in those, I set the 3 settings to false in my ini file.

[Main]
...
gsa=False
pooled_gsa=False
anonymous=False
compress=1

However, the pipeline still assembles, pools and bins the reads despite setting them to False as shown above. Is there a way to avoid running these steps as they take some time (~1h for 4G x 2 samples dataset). I am using the most recent git clone (as of May 11th, 2022).

PS. Is there a setting to output separate pooled PE files instead of the interleaved one? I think using anonymous=False produces separate PE genome files. I would like to have just the separate but pooled PE files.

Much appreciated.
Hazem Sharaf

[AlphaSquad]

Hi Hazem,

thank you for your report, that obviously should not be like that. I will investigate and come back to you and hopefully there is a quick fix.
Regarding the interleaved/split files: The easiest solution here is probably to just a method to split the file "manually", e.g. seqkit