StrainPhlan sample2markers.py loading database

Microbial community profiling StrainPhlAn
1

Hi,
I find that the process of loading the database is consuming a significant amount of time when running a script like sample2markers.py , and I wish to prevent the database from being reloaded with each function call. Could you please help me solve that? Thanks for your advice

Fri Jul 12 11:27:32 2024: Loading MetaPhlAn mpa_vJun23_CHOCOPhlAnSGB_202403 database…
Fri Jul 12 11:28:20 2024: Done.
Fri Jul 12 11:29:32 2024: Done.

2

Hi, in the newest version of StrainPhlAn 4.1 the speed is much optimized. You can pass multiple samples to -i/–input separated by space and the database will load just once. Moreover on a multi-cpu/thread system you can parallelize those multiple samples with the parameter -n/–nprocs.