Closed Joebio closed 1 year ago
Hi Joe,
Indeed this tool can take time depending on the number of reads and the number of OTU. Unfortunatly you can not do anything to improve it. For information, this tool is not parallelised so using 4 threads is useless (I guess that something to work on).
Regards
Maria
Okay, I see. Thank you so much.
Best regards Joe
Hi team!
I'm normalising in BIOM by random sampling (after the clustering step) using normalisation.py in version 3.2.3 under 4 threads and 8Gb of RAM. It has been running for almost 48 hours, I am wondering if there is any way I can use to reduce the running time.
The command I am using is:
normalisation.py -n 25659 -i clustering.biom -f clustering.fasta -b normalisation_abundance.biom -o normalisation.fasta -s normalisation.html -l normalisation.log
The biom file is representing 33 samples and the largest sample size is around 182,736 reads of V3-V4 16S.
TIA. Joe