FAQ

1. Why just few reads map in my profiles?

If you profile your samples and have zero reads mapping or very few reads with the -c option. One possibility is that all the reads are filtered out. The mOTUs profiler is filtering out all the reads that map with less than 75 nucleotides (-l 75). For example, with old samples, the fastq reads were on average of length 50, and in this case they would all be filtered out. Try to use -l 45 to keep more reads during the filtering process.
Note that the average read length of the reads in your sample is printed by the tool:

[main] Minimum alignment length: 75 (average read length: 50)

You can also add -g 1 to keep more reads (see Increase precision or recall page for more information).
Another possibility is that you are profiling samples from a biome that is not covered by reference genomes and is also not covered by mOTUs. The biomes that we can currently profile with meta-mOTUs (unknown species) are oceans, human gut, human oral cavity, human vagina and human skin. If you have soil samples, mOTUs will be able to profile only the reference genomes, which will cover a small portion of all the species.