the use of the -ci parameter

[SUPERI-SAI]

Hi, I am very confused about the use of the -ci parameter. In the first step, in order to obtain the specific kmers of each genome, I used KMC to compare the two genomes, using the following command with the default -ci2: kmc -t20 -k13 -fm -cs1000000000 Nepal.fa Nepal_out Nepal_temp kmc -t20 -k13 -fm -cs1000000000 ZG.fasta ZG_out ZG_temp

here is the result: ZG_specific.txt Nepal_specific.txt

when i changed the "-ci": kmc -t20 -k13 -fm -ci100 -cs1000000000 Nepal.fa Nepal_out Nepal_temp kmc -t20 -k13 -fm -ci100 -cs1000000000 ZG.fasta ZG_out ZG_temp the result is very strange: Nepal_specific.txt ZG_specific.part.txt.gz

As the function of "-ci" is: -ci - exclude k-mers occurring less than times (default: 2) I thought that using "-ci100" would produce only a fraction of the "-ci2" result (kmers that produces more than 100 times), but it doesn't seem to. The result of "-CI100" is much larger than the result of "-CI2". Why does this happen?

Can you help me figure out where the error is? Thanks! YYY