i use humann3 to ran my data(14 GB),but the info show thatTotal species selected from prescreen: 14,it is too small for my data, why it happened?my code as following:
humann --input /mnt/qc/F/1H/1H.fastq --output /mnt/gongneng/humann/F/1H --threads 16 --metaphlan-options="--bowtie2db /mnt/shujuku/humann3/metaphlan/v30 --index mpa_v30_CHOCOPhlAn_201901" --diamond-options="--index-chunks 1 --block-size 3" --memory-use maximum
just now, i use metaphlan4 with humann3, is show Total species selected from prescreen: 558, it because the metaphlan4 have more larger database than metaphlan3?
Yes, metaphlan 4 has a way larger database in comparison with version 3, please, have a look at our latest publication Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 | Nature Biotechnology