Comments (4)
aphillippy
commented on July 20, 2024
Hey Darya, yes, that genome size looks completely wonky. We'll take a look. Thanks!
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tseemann
commented on July 20, 2024
I just got the same thing on a massive collection of S.aureus genomes:
WARNING: For the k-mer size used (21), the random match probability (0.000641033) is above the specified warning threshold (0.01) for the sequence "saureus" of size 18446744072235684419. Distances to this sequence may be underestimated as a result. To meet the threshold of 0.01, a k-mer size of at least 20 is required.
The sequence size is ~16 Gbp of contigs.
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tseemann
commented on July 20, 2024
Ok, I built head with your 64 bit int patch and it now sketches them ok. 6aad387
Can you make a 1.0.2 release?
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ondovb
commented on July 20, 2024
Fixed in v1.0.2
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Related Issues (20)
- how many genomes can the mash deal with?
- Update RefSeq? HOT 2
- output the containment sequence HOT 3
- Sorting on mash-distance HOT 1
- Sketching paired- and single-end reads together
- Inconsistent number of matching hashes HOT 1
- Are Mash distances always symmetric?
- Missing include limits
- Mash dist -p, wrong number of threads (bug?)
- m1 ARM support?
- Cannot update Mash from version 1.1 to version 2
- -M for weighted kmer
- Can Mash accurately classify subspecies? HOT 1
- Doubts when using mash on multiple assemblies HOT 1
- MASH distance for AA
- Explanation of the .msh format HOT 2
- The release version of refseq.genomes.k21.s1000.msh
- Argument list too long HOT 2
- Distance between two genomes not consistent when I chnage the rest of the dataset. HOT 2
- Add brief description about what MASH does to the README.md
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