Hello, I use taxnometer，could you please tell me which parameters you used for MMseqs2? I have downloaded the gastrointestinal dataset. After obtaining the contig and abundance files, I ran MMseqs2 using the following commands:
1.mmseqs createdb contigs.fna.gz queryDB
2.mmseqs taxonomy mmseqs_work/queryDB databases/GTDB resultDB tmp_2 --tax-lineage 1
3.mmseqs createtsv /disk1/user/Taxnometer/vamb/data/mmseqs_work/queryDB databases/GTDB
4./disk1/user/Taxnometer/vamb/data/mmseqs_work/resultDB taxonomy_mmseqs.tsv
However, I only obtained an F1-score of around 0.65. Could you please advise where the problem might be?
Hello, I use taxnometer，could you please tell me which parameters you used for MMseqs2? I have downloaded the gastrointestinal dataset. After obtaining the contig and abundance files, I ran MMseqs2 using the following commands:
1.mmseqs createdb contigs.fna.gz queryDB
2.mmseqs taxonomy mmseqs_work/queryDB databases/GTDB resultDB tmp_2 --tax-lineage 1
3.mmseqs createtsv /disk1/user/Taxnometer/vamb/data/mmseqs_work/queryDB databases/GTDB
4./disk1/user/Taxnometer/vamb/data/mmseqs_work/resultDB taxonomy_mmseqs.tsv
However, I only obtained an F1-score of around 0.65. Could you please advise where the problem might be?