Garbage kmer results for short sequences

[tseemann]

I am getting false kmer counts with simple examples like the one below.

1. AAA=255, but should be AAA=1 ?
2. Total kmers should be 10 not 32659 ?
3. Total no. of reads should be 1 not 2 ?

If I change to -ci0 then i get 32525 fake k-mers. if I change to -p5 i get 32706 fakes. Might be related to #103

$ cat seq3.fa
>seq3
AAACCCAACCAC

$ kmc -ci1 -k3 -fa -seq3.fa seq3 /tmp/
Stage 1: 100%
1st stage: 0.002712s
2nd stage: 0.00102s
Total    : 0.003732s
Tmp size : 0MB

Stats:
   No. of k-mers below min. threshold :            0
   No. of k-mers above max. threshold :            0
   No. of unique k-mers               :            8
   No. of unique counted k-mers       :            8
   Total no. of k-mers                :        32659
   Total no. of reads                 :            2
   Total no. of super-k-mers          :            0

$ kmc_dump seq3 /dev/stdout
AAA     255
AAC     2
ACA     1
ACC     2
CAA     2
CAC     1
CCA     2
CCC     1

[tseemann]

UPDATE:

If I change it to -fm (multi-fasta, even though only 1 sequence) it seems to do better, but still wrong.

   No. of k-mers below min. threshold :            0
   No. of k-mers above max. threshold :            0
   No. of unique k-mers               :            7
   No. of unique counted k-mers       :            7
   Total no. of k-mers                :           10
   Total no. of sequences             :            1
   Total no. of super-k-mers          :            0

[marekkokot]

Thanks for reporting that. What is the number of cores on your machine? On my machine results are also incorrect, but not exactly as same as what you reported.
I have also checked with -fm switch and get the same results as you. Why do you think they are incorrect, because at first look it seems OK to me. Am I missing something?

[marekkokot]

Hi, I think 85ad76956d890aa24fc8525eee5653078ed86ace should fix the issue. Could you please verify it on your environment and let me know?

[tseemann]

I have 72 cores.

I can only test tagged versions.

git tag v3.3.2
git push --tags

?

[marekkokot]

I have tagged this version.

[tseemann]

Thank you!