Remove precomputed data assets, configurations, and documentation
This change removes precomputed model parameters, phylogenetic tree datasets, k-mer spectrum data, and compressed profile archives. It also deletes runtime logs and detailed pipeline documentation. The repository ignore list is updated to exclude the sandbox directory.
This commit is contained in:
Eric Coissac
@@ -5,6 +5,7 @@
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.serena/
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.serena/
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.zed/
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.zed/
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memory/
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memory/
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sandbox/
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src/target
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src/target
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data-stress
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data-stress
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*.fasta
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*.fasta
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@@ -1,167 +0,0 @@
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ratio_ceiling: 0.5
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cardinality_transitions:
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- from: 0
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to: 0
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count: 122014779
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probability: 0.870049812090934
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- from: 0
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to: 1
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count: 17966272
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probability: 0.12811195254940888
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- from: 0
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to: 2
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||||||
count: 233683
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||||||
probability: 0.001666321505518981
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||||||
- from: 0
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||||||
to: 3
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||||||
count: 24109
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||||||
probability: 0.00017191385413811494
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||||||
- from: 0
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||||||
to: 4
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||||||
count: 0
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||||||
probability: 0.0
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||||||
- from: 1
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||||||
to: 0
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||||||
count: 17966272
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||||||
probability: 0.967023782579572
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||||||
- from: 1
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||||||
to: 1
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||||||
count: 602798
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||||||
probability: 0.03244523972983381
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||||||
- from: 1
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||||||
to: 2
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||||||
count: 9562
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||||||
probability: 0.0005146688978673966
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||||||
- from: 1
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||||||
to: 3
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||||||
count: 303
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||||||
probability: 0.00001630879272681669
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||||||
- from: 1
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||||||
to: 4
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||||||
count: 0
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||||||
probability: 0.0
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||||||
- from: 2
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||||||
to: 0
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||||||
count: 233683
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||||||
probability: 0.9585500516842502
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||||||
- from: 2
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||||||
to: 1
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||||||
count: 9562
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||||||
probability: 0.039222603245442765
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||||||
- from: 2
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||||||
to: 2
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||||||
count: 438
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||||||
probability: 0.0017966429848885097
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- from: 2
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||||||
to: 3
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||||||
count: 105
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||||||
probability: 0.00043070208541847837
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||||||
- from: 2
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||||||
to: 4
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||||||
count: 0
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||||||
probability: 0.0
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||||||
- from: 3
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||||||
to: 0
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||||||
count: 24109
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||||||
probability: 0.9827171564831044
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||||||
- from: 3
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||||||
to: 1
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||||||
count: 303
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||||||
probability: 0.012350711286838137
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||||||
- from: 3
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||||||
to: 2
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||||||
count: 105
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||||||
probability: 0.004279949455834998
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||||||
- from: 3
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||||||
to: 3
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||||||
count: 16
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||||||
probability: 0.0006521827742224758
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||||||
- from: 3
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||||||
to: 4
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||||||
count: 0
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||||||
probability: 0.0
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||||||
- from: 4
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||||||
to: 0
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||||||
count: 0
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||||||
probability: 0.0
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||||||
- from: 4
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||||||
to: 1
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||||||
count: 0
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||||||
probability: 0.0
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||||||
- from: 4
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to: 2
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count: 0
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||||||
probability: 0.0
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- from: 4
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to: 3
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count: 0
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||||||
probability: 0.0
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- from: 4
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to: 4
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count: 0
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probability: 0.0
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composition_transitions:
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- from: 'A'
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to: 'A'
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count: 0
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||||||
probability: 0.0
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- from: 'A'
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to: 'C'
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count: 0
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||||||
probability: 0.0
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- from: 'A'
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to: 'G'
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||||||
count: 0
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probability: 0.0
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||||||
- from: 'A'
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||||||
to: 'T'
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||||||
count: 0
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||||||
probability: 0.0
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||||||
- from: 'C'
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||||||
to: 'A'
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count: 0
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probability: 0.0
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- from: 'C'
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to: 'C'
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count: 96389
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probability: 0.9663832688335907
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- from: 'C'
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to: 'G'
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count: 1290
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probability: 0.012933368089671353
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- from: 'C'
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to: 'T'
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count: 2063
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probability: 0.020683363076737984
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- from: 'G'
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to: 'A'
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count: 0
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||||||
probability: 0.0
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||||||
- from: 'G'
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to: 'C'
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count: 1290
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probability: 0.005696948820201646
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- from: 'G'
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to: 'G'
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count: 222720
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probability: 0.9835848381669073
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- from: 'G'
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to: 'T'
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count: 2427
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probability: 0.010718213012891003
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- from: 'T'
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to: 'A'
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count: 0
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probability: 0.0
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||||||
- from: 'T'
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||||||
to: 'C'
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||||||
count: 2063
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||||||
probability: 0.007305266661709142
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||||||
- from: 'T'
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||||||
to: 'G'
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||||||
count: 2427
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||||||
probability: 0.008594223067362136
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||||||
- from: 'T'
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||||||
to: 'T'
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count: 277909
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probability: 0.9841005102709287
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@@ -1,167 +0,0 @@
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ratio_ceiling: 0.5
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cardinality_transitions:
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- from: 0
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||||||
to: 0
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count: 13019012
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||||||
probability: 0.8682962128540935
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||||||
- from: 0
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||||||
to: 1
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||||||
count: 1945560
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||||||
probability: 0.12975810913150784
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||||||
- from: 0
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||||||
to: 2
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||||||
count: 26381
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||||||
probability: 0.0017594670310852958
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||||||
- from: 0
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||||||
to: 3
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||||||
count: 2792
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||||||
probability: 0.000186210983313375
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||||||
- from: 0
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||||||
to: 4
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||||||
count: 0
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||||||
probability: 0.0
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||||||
- from: 1
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||||||
to: 0
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||||||
count: 1945560
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||||||
probability: 0.9666005228573729
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||||||
- from: 1
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||||||
to: 1
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||||||
count: 66078
|
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||||||
probability: 0.03282912341401421
|
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||||||
- from: 1
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||||||
to: 2
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||||||
count: 1123
|
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||||||
probability: 0.0005579331334776772
|
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||||||
- from: 1
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||||||
to: 3
|
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||||||
count: 25
|
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||||||
probability: 0.000012420595135300028
|
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||||||
- from: 1
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||||||
to: 4
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||||||
count: 0
|
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||||||
probability: 0.0
|
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||||||
- from: 2
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||||||
to: 0
|
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||||||
count: 26381
|
|
||||||
probability: 0.9567346050627402
|
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||||||
- from: 2
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||||||
to: 1
|
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||||||
count: 1123
|
|
||||||
probability: 0.04072677159643142
|
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||||||
- from: 2
|
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||||||
to: 2
|
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||||||
count: 51
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||||||
probability: 0.0018495684340320592
|
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||||||
- from: 2
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||||||
to: 3
|
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||||||
count: 19
|
|
||||||
probability: 0.0006890549067962574
|
|
||||||
- from: 2
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||||||
to: 4
|
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||||||
count: 0
|
|
||||||
probability: 0.0
|
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||||||
- from: 3
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||||||
to: 0
|
|
||||||
count: 2792
|
|
||||||
probability: 0.9841381741275996
|
|
||||||
- from: 3
|
|
||||||
to: 1
|
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||||||
count: 25
|
|
||||||
probability: 0.008812125484666901
|
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||||||
- from: 3
|
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||||||
to: 2
|
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||||||
count: 19
|
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||||||
probability: 0.0066972153683468455
|
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||||||
- from: 3
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||||||
to: 3
|
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||||||
count: 1
|
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||||||
probability: 0.00035248501938667606
|
|
||||||
- from: 3
|
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||||||
to: 4
|
|
||||||
count: 0
|
|
||||||
probability: 0.0
|
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||||||
- from: 4
|
|
||||||
to: 0
|
|
||||||
count: 0
|
|
||||||
probability: 0.0
|
|
||||||
- from: 4
|
|
||||||
to: 1
|
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||||||
count: 0
|
|
||||||
probability: 0.0
|
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||||||
- from: 4
|
|
||||||
to: 2
|
|
||||||
count: 0
|
|
||||||
probability: 0.0
|
|
||||||
- from: 4
|
|
||||||
to: 3
|
|
||||||
count: 0
|
|
||||||
probability: 0.0
|
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||||||
- from: 4
|
|
||||||
to: 4
|
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||||||
count: 0
|
|
||||||
probability: 0.0
|
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||||||
composition_transitions:
|
|
||||||
- from: 'A'
|
|
||||||
to: 'A'
|
|
||||||
count: 0
|
|
||||||
probability: 0.0
|
|
||||||
- from: 'A'
|
|
||||||
to: 'C'
|
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||||||
count: 0
|
|
||||||
probability: 0.0
|
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||||||
- from: 'A'
|
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||||||
to: 'G'
|
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||||||
count: 0
|
|
||||||
probability: 0.0
|
|
||||||
- from: 'A'
|
|
||||||
to: 'T'
|
|
||||||
count: 0
|
|
||||||
probability: 0.0
|
|
||||||
- from: 'C'
|
|
||||||
to: 'A'
|
|
||||||
count: 0
|
|
||||||
probability: 0.0
|
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||||||
- from: 'C'
|
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||||||
to: 'C'
|
|
||||||
count: 10771
|
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||||||
probability: 0.9619540948468339
|
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||||||
- from: 'C'
|
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||||||
to: 'G'
|
|
||||||
count: 163
|
|
||||||
probability: 0.014557470751094042
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||||||
- from: 'C'
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|
||||||
to: 'T'
|
|
||||||
count: 263
|
|
||||||
probability: 0.023488434402071982
|
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||||||
- from: 'G'
|
|
||||||
to: 'A'
|
|
||||||
count: 0
|
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||||||
probability: 0.0
|
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||||||
- from: 'G'
|
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||||||
to: 'C'
|
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||||||
count: 163
|
|
||||||
probability: 0.006662851536952256
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||||||
- from: 'G'
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||||||
to: 'G'
|
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||||||
count: 24073
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|
||||||
probability: 0.9840173315892741
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|
||||||
- from: 'G'
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||||||
to: 'T'
|
|
||||||
count: 228
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||||||
probability: 0.009319816873773708
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||||||
- from: 'T'
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|
||||||
to: 'A'
|
|
||||||
count: 0
|
|
||||||
probability: 0.0
|
|
||||||
- from: 'T'
|
|
||||||
to: 'C'
|
|
||||||
count: 263
|
|
||||||
probability: 0.008464484567603231
|
|
||||||
- from: 'T'
|
|
||||||
to: 'G'
|
|
||||||
count: 228
|
|
||||||
probability: 0.007338032248720672
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|
||||||
- from: 'T'
|
|
||||||
to: 'T'
|
|
||||||
count: 30580
|
|
||||||
probability: 0.9841974831836761
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@@ -1,275 +0,0 @@
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[2m2026-04-27T20:36:04.208955Z[0m [32m INFO[0m [2mobikmer::cmd::partition[0m[2m:[0m dereplicating...
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[2m2026-04-27T20:36:11.471489Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 0/256
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[2m2026-04-27T20:36:11.471521Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 128/256
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||||||
[2m2026-04-27T20:36:11.471530Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 32/256
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||||||
[2m2026-04-27T20:36:11.471535Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 12/256
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||||||
[2m2026-04-27T20:36:11.471551Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 76/256
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[2m2026-04-27T20:36:11.471522Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 2/256
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||||||
[2m2026-04-27T20:36:11.471525Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 4/256
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||||||
[2m2026-04-27T20:36:11.471535Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 96/256
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[2m2026-04-27T20:36:11.471535Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 80/256
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||||||
[2m2026-04-27T20:36:11.471535Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 10/256
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||||||
[2m2026-04-27T20:36:11.471538Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 16/256
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||||||
[2m2026-04-27T20:36:11.471543Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 224/256
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||||||
[2m2026-04-27T20:36:11.471537Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 192/256
|
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||||||
[2m2026-04-27T20:36:11.471536Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 64/256
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||||||
[2m2026-04-27T20:36:11.471537Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 72/256
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||||||
[2m2026-04-27T20:36:11.471530Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 8/256
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||||||
[2m2026-04-27T20:36:12.831739Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 129/256
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||||||
[2m2026-04-27T20:36:13.555104Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 9/256
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||||||
[2m2026-04-27T20:36:14.077082Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 17/256
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||||||
[2m2026-04-27T20:36:14.203310Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 77/256
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||||||
[2m2026-04-27T20:36:14.316403Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 3/256
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||||||
[2m2026-04-27T20:36:14.415177Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 33/256
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||||||
[2m2026-04-27T20:36:14.467689Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 97/256
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||||||
[2m2026-04-27T20:36:14.559650Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 5/256
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|
||||||
[2m2026-04-27T20:36:14.591431Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 81/256
|
|
||||||
[2m2026-04-27T20:36:14.606508Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 193/256
|
|
||||||
[2m2026-04-27T20:36:14.611406Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 73/256
|
|
||||||
[2m2026-04-27T20:36:14.623813Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 11/256
|
|
||||||
[2m2026-04-27T20:36:14.665058Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 65/256
|
|
||||||
[2m2026-04-27T20:36:14.666877Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 1/256
|
|
||||||
[2m2026-04-27T20:36:14.667569Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 13/256
|
|
||||||
[2m2026-04-27T20:36:14.697486Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 225/256
|
|
||||||
[2m2026-04-27T20:36:14.698441Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 130/256
|
|
||||||
[2m2026-04-27T20:36:14.998749Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 14/256
|
|
||||||
[2m2026-04-27T20:36:15.485303Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 18/256
|
|
||||||
[2m2026-04-27T20:36:15.637613Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 78/256
|
|
||||||
[2m2026-04-27T20:36:15.722825Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 98/256
|
|
||||||
[2m2026-04-27T20:36:15.831703Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 112/256
|
|
||||||
[2m2026-04-27T20:36:16.161408Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 66/256
|
|
||||||
[2m2026-04-27T20:36:16.340113Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 226/256
|
|
||||||
[2m2026-04-27T20:36:16.506407Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 82/256
|
|
||||||
[2m2026-04-27T20:36:16.542430Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 74/256
|
|
||||||
[2m2026-04-27T20:36:16.550654Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 34/256
|
|
||||||
[2m2026-04-27T20:36:16.634719Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 6/256
|
|
||||||
[2m2026-04-27T20:36:16.763833Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 194/256
|
|
||||||
[2m2026-04-27T20:36:16.813285Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 131/256
|
|
||||||
[2m2026-04-27T20:36:16.913975Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 208/256
|
|
||||||
[2m2026-04-27T20:36:16.993526Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 15/256
|
|
||||||
[2m2026-04-27T20:36:17.092998Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 160/256
|
|
||||||
[2m2026-04-27T20:36:17.114964Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 88/256
|
|
||||||
[2m2026-04-27T20:36:17.148685Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 79/256
|
|
||||||
[2m2026-04-27T20:36:17.161989Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 19/256
|
|
||||||
[2m2026-04-27T20:36:17.180022Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 113/256
|
|
||||||
[2m2026-04-27T20:36:17.397037Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 67/256
|
|
||||||
[2m2026-04-27T20:36:17.484519Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 99/256
|
|
||||||
[2m2026-04-27T20:36:17.906842Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 35/256
|
|
||||||
[2m2026-04-27T20:36:18.146262Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 75/256
|
|
||||||
[2m2026-04-27T20:36:18.247130Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 7/256
|
|
||||||
[2m2026-04-27T20:36:18.303872Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 227/256
|
|
||||||
[2m2026-04-27T20:36:18.374448Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 195/256
|
|
||||||
[2m2026-04-27T20:36:18.382279Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 83/256
|
|
||||||
[2m2026-04-27T20:36:18.428092Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 104/256
|
|
||||||
[2m2026-04-27T20:36:18.442213Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 132/256
|
|
||||||
[2m2026-04-27T20:36:18.621883Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 209/256
|
|
||||||
[2m2026-04-27T20:36:18.784307Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 161/256
|
|
||||||
[2m2026-04-27T20:36:18.796465Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 114/256
|
|
||||||
[2m2026-04-27T20:36:18.877587Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 120/256
|
|
||||||
[2m2026-04-27T20:36:18.888423Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 89/256
|
|
||||||
[2m2026-04-27T20:36:18.918340Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 20/256
|
|
||||||
[2m2026-04-27T20:36:18.985341Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 100/256
|
|
||||||
[2m2026-04-27T20:36:19.080092Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 68/256
|
|
||||||
[2m2026-04-27T20:36:19.282760Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 36/256
|
|
||||||
[2m2026-04-27T20:36:19.485079Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 92/256
|
|
||||||
[2m2026-04-27T20:36:19.692354Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 24/256
|
|
||||||
[2m2026-04-27T20:36:19.746458Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 228/256
|
|
||||||
[2m2026-04-27T20:36:20.004054Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 84/256
|
|
||||||
[2m2026-04-27T20:36:20.164510Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 196/256
|
|
||||||
[2m2026-04-27T20:36:20.277288Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 105/256
|
|
||||||
[2m2026-04-27T20:36:20.349391Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 133/256
|
|
||||||
[2m2026-04-27T20:36:20.511981Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 210/256
|
|
||||||
[2m2026-04-27T20:36:20.709583Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 101/256
|
|
||||||
[2m2026-04-27T20:36:20.715870Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 69/256
|
|
||||||
[2m2026-04-27T20:36:20.728029Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 115/256
|
|
||||||
[2m2026-04-27T20:36:20.822257Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 162/256
|
|
||||||
[2m2026-04-27T20:36:20.982131Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 90/256
|
|
||||||
[2m2026-04-27T20:36:20.990122Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 21/256
|
|
||||||
[2m2026-04-27T20:36:21.030814Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 121/256
|
|
||||||
[2m2026-04-27T20:36:21.088309Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 93/256
|
|
||||||
[2m2026-04-27T20:36:21.134904Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 37/256
|
|
||||||
[2m2026-04-27T20:36:21.196814Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 25/256
|
|
||||||
[2m2026-04-27T20:36:21.444384Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 85/256
|
|
||||||
[2m2026-04-27T20:36:21.605343Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 197/256
|
|
||||||
[2m2026-04-27T20:36:21.954010Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 106/256
|
|
||||||
[2m2026-04-27T20:36:22.026167Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 229/256
|
|
||||||
[2m2026-04-27T20:36:22.194676Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 134/256
|
|
||||||
[2m2026-04-27T20:36:22.209911Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 211/256
|
|
||||||
[2m2026-04-27T20:36:22.281984Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 70/256
|
|
||||||
[2m2026-04-27T20:36:22.440637Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 163/256
|
|
||||||
[2m2026-04-27T20:36:22.481750Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 91/256
|
|
||||||
[2m2026-04-27T20:36:22.522458Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 116/256
|
|
||||||
[2m2026-04-27T20:36:22.775669Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 22/256
|
|
||||||
[2m2026-04-27T20:36:23.095766Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 102/256
|
|
||||||
[2m2026-04-27T20:36:23.119802Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 94/256
|
|
||||||
[2m2026-04-27T20:36:23.183138Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 122/256
|
|
||||||
[2m2026-04-27T20:36:23.186904Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 38/256
|
|
||||||
[2m2026-04-27T20:36:23.196250Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 86/256
|
|
||||||
[2m2026-04-27T20:36:23.206118Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 26/256
|
|
||||||
[2m2026-04-27T20:36:23.314520Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 198/256
|
|
||||||
[2m2026-04-27T20:36:23.355959Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 107/256
|
|
||||||
[2m2026-04-27T20:36:23.526146Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 230/256
|
|
||||||
[2m2026-04-27T20:36:23.723572Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 212/256
|
|
||||||
[2m2026-04-27T20:36:23.856569Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 71/256
|
|
||||||
[2m2026-04-27T20:36:23.910613Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 164/256
|
|
||||||
[2m2026-04-27T20:36:23.945560Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 135/256
|
|
||||||
[2m2026-04-27T20:36:24.085073Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 117/256
|
|
||||||
[2m2026-04-27T20:36:24.111144Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 144/256
|
|
||||||
[2m2026-04-27T20:36:24.188547Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 23/256
|
|
||||||
[2m2026-04-27T20:36:24.573867Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 103/256
|
|
||||||
[2m2026-04-27T20:36:24.604461Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 27/256
|
|
||||||
[2m2026-04-27T20:36:24.670189Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 95/256
|
|
||||||
[2m2026-04-27T20:36:24.935767Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 123/256
|
|
||||||
[2m2026-04-27T20:36:25.031507Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 39/256
|
|
||||||
[2m2026-04-27T20:36:25.039809Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 108/256
|
|
||||||
[2m2026-04-27T20:36:25.067950Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 199/256
|
|
||||||
[2m2026-04-27T20:36:25.149100Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 231/256
|
|
||||||
[2m2026-04-27T20:36:25.272346Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 213/256
|
|
||||||
[2m2026-04-27T20:36:25.400111Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 165/256
|
|
||||||
[2m2026-04-27T20:36:25.607381Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 136/256
|
|
||||||
[2m2026-04-27T20:36:25.902415Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 152/256
|
|
||||||
[2m2026-04-27T20:36:26.055400Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 118/256
|
|
||||||
[2m2026-04-27T20:36:26.138877Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 119/256
|
|
||||||
[2m2026-04-27T20:36:26.255235Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 87/256
|
|
||||||
[2m2026-04-27T20:36:26.350364Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 148/256
|
|
||||||
[2m2026-04-27T20:36:26.465089Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 145/256
|
|
||||||
[2m2026-04-27T20:36:26.682375Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 40/256
|
|
||||||
[2m2026-04-27T20:36:26.694729Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 216/256
|
|
||||||
[2m2026-04-27T20:36:26.777197Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 28/256
|
|
||||||
[2m2026-04-27T20:36:26.802996Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 124/256
|
|
||||||
[2m2026-04-27T20:36:26.972099Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 200/256
|
|
||||||
[2m2026-04-27T20:36:27.066713Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 232/256
|
|
||||||
[2m2026-04-27T20:36:27.112569Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 166/256
|
|
||||||
[2m2026-04-27T20:36:27.156124Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 214/256
|
|
||||||
[2m2026-04-27T20:36:27.231214Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 137/256
|
|
||||||
[2m2026-04-27T20:36:27.359784Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 109/256
|
|
||||||
[2m2026-04-27T20:36:27.369743Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 153/256
|
|
||||||
[2m2026-04-27T20:36:27.668409Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 204/256
|
|
||||||
[2m2026-04-27T20:36:27.701887Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 202/256
|
|
||||||
[2m2026-04-27T20:36:27.794402Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 215/256
|
|
||||||
[2m2026-04-27T20:36:28.058391Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 149/256
|
|
||||||
[2m2026-04-27T20:36:28.192195Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 217/256
|
|
||||||
[2m2026-04-27T20:36:28.369717Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 125/256
|
|
||||||
[2m2026-04-27T20:36:28.412339Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 41/256
|
|
||||||
[2m2026-04-27T20:36:28.496068Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 29/256
|
|
||||||
[2m2026-04-27T20:36:28.693510Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 167/256
|
|
||||||
[2m2026-04-27T20:36:28.808495Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 201/256
|
|
||||||
[2m2026-04-27T20:36:28.843564Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 233/256
|
|
||||||
[2m2026-04-27T20:36:28.917920Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 140/256
|
|
||||||
[2m2026-04-27T20:36:28.940416Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 138/256
|
|
||||||
[2m2026-04-27T20:36:29.125956Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 110/256
|
|
||||||
[2m2026-04-27T20:36:29.197246Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 154/256
|
|
||||||
[2m2026-04-27T20:36:29.376894Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 203/256
|
|
||||||
[2m2026-04-27T20:36:29.491887Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 176/256
|
|
||||||
[2m2026-04-27T20:36:29.501763Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 205/256
|
|
||||||
[2m2026-04-27T20:36:29.538499Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 150/256
|
|
||||||
[2m2026-04-27T20:36:29.685646Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 218/256
|
|
||||||
[2m2026-04-27T20:36:29.874786Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 126/256
|
|
||||||
[2m2026-04-27T20:36:30.021059Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 42/256
|
|
||||||
[2m2026-04-27T20:36:30.255780Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 240/256
|
|
||||||
[2m2026-04-27T20:36:30.602468Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 141/256
|
|
||||||
[2m2026-04-27T20:36:30.696718Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 234/256
|
|
||||||
[2m2026-04-27T20:36:30.784522Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 139/256
|
|
||||||
[2m2026-04-27T20:36:31.027016Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 155/256
|
|
||||||
[2m2026-04-27T20:36:31.073326Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 30/256
|
|
||||||
[2m2026-04-27T20:36:31.137264Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 111/256
|
|
||||||
[2m2026-04-27T20:36:31.143413Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 168/256
|
|
||||||
[2m2026-04-27T20:36:31.237329Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 206/256
|
|
||||||
[2m2026-04-27T20:36:31.252908Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 236/256
|
|
||||||
[2m2026-04-27T20:36:31.306110Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 177/256
|
|
||||||
[2m2026-04-27T20:36:31.431064Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 151/256
|
|
||||||
[2m2026-04-27T20:36:31.490837Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 127/256
|
|
||||||
[2m2026-04-27T20:36:31.528815Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 43/256
|
|
||||||
[2m2026-04-27T20:36:31.790858Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 219/256
|
|
||||||
[2m2026-04-27T20:36:31.803934Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 241/256
|
|
||||||
[2m2026-04-27T20:36:32.131051Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 156/256
|
|
||||||
[2m2026-04-27T20:36:32.433342Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 235/256
|
|
||||||
[2m2026-04-27T20:36:32.459699Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 142/256
|
|
||||||
[2m2026-04-27T20:36:32.532717Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 31/256
|
|
||||||
[2m2026-04-27T20:36:32.814909Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 184/256
|
|
||||||
[2m2026-04-27T20:36:32.967090Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 169/256
|
|
||||||
[2m2026-04-27T20:36:33.062660Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 178/256
|
|
||||||
[2m2026-04-27T20:36:33.076014Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 237/256
|
|
||||||
[2m2026-04-27T20:36:33.128961Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 207/256
|
|
||||||
[2m2026-04-27T20:36:33.228734Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 180/256
|
|
||||||
[2m2026-04-27T20:36:33.228905Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 143/256
|
|
||||||
[2m2026-04-27T20:36:33.266931Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 44/256
|
|
||||||
[2m2026-04-27T20:36:33.280333Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 158/256
|
|
||||||
[2m2026-04-27T20:36:33.368740Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 220/256
|
|
||||||
[2m2026-04-27T20:36:33.373469Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 179/256
|
|
||||||
[2m2026-04-27T20:36:33.409455Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 157/256
|
|
||||||
[2m2026-04-27T20:36:33.685036Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 242/256
|
|
||||||
[2m2026-04-27T20:36:34.174714Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 182/256
|
|
||||||
[2m2026-04-27T20:36:34.255362Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 146/256
|
|
||||||
[2m2026-04-27T20:36:34.284053Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 170/256
|
|
||||||
[2m2026-04-27T20:36:34.340602Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 185/256
|
|
||||||
[2m2026-04-27T20:36:34.748830Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 45/256
|
|
||||||
[2m2026-04-27T20:36:34.894515Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 172/256
|
|
||||||
[2m2026-04-27T20:36:35.342815Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 238/256
|
|
||||||
[2m2026-04-27T20:36:35.549647Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 159/256
|
|
||||||
[2m2026-04-27T20:36:35.556431Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 181/256
|
|
||||||
[2m2026-04-27T20:36:35.579877Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 188/256
|
|
||||||
[2m2026-04-27T20:36:35.619438Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 221/256
|
|
||||||
[2m2026-04-27T20:36:35.704344Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 174/256
|
|
||||||
[2m2026-04-27T20:36:35.891634Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 190/256
|
|
||||||
[2m2026-04-27T20:36:35.893065Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 239/256
|
|
||||||
[2m2026-04-27T20:36:35.978053Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 183/256
|
|
||||||
[2m2026-04-27T20:36:35.980835Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 186/256
|
|
||||||
[2m2026-04-27T20:36:36.010364Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 243/256
|
|
||||||
[2m2026-04-27T20:36:36.084972Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 171/256
|
|
||||||
[2m2026-04-27T20:36:36.085806Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 147/256
|
|
||||||
[2m2026-04-27T20:36:36.129893Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 48/256
|
|
||||||
[2m2026-04-27T20:36:36.188339Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 46/256
|
|
||||||
[2m2026-04-27T20:36:36.281975Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 173/256
|
|
||||||
[2m2026-04-27T20:36:37.004395Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 187/256
|
|
||||||
[2m2026-04-27T20:36:37.080479Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 222/256
|
|
||||||
[2m2026-04-27T20:36:37.100573Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 189/256
|
|
||||||
[2m2026-04-27T20:36:37.422152Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 248/256
|
|
||||||
[2m2026-04-27T20:36:37.446786Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 175/256
|
|
||||||
[2m2026-04-27T20:36:37.951518Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 244/256
|
|
||||||
[2m2026-04-27T20:36:38.235613Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 191/256
|
|
||||||
[2m2026-04-27T20:36:38.259288Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 47/256
|
|
||||||
[2m2026-04-27T20:36:38.379966Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 252/256
|
|
||||||
[2m2026-04-27T20:36:38.380690Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 223/256
|
|
||||||
[2m2026-04-27T20:36:38.520398Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 56/256
|
|
||||||
[2m2026-04-27T20:36:38.598256Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 49/256
|
|
||||||
[2m2026-04-27T20:36:38.680704Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 254/256
|
|
||||||
[2m2026-04-27T20:36:38.681038Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 246/256
|
|
||||||
[2m2026-04-27T20:36:38.813533Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 247/256
|
|
||||||
[2m2026-04-27T20:36:38.820199Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 60/256
|
|
||||||
[2m2026-04-27T20:36:38.961240Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 52/256
|
|
||||||
[2m2026-04-27T20:36:39.001585Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 58/256
|
|
||||||
[2m2026-04-27T20:36:39.050047Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 249/256
|
|
||||||
[2m2026-04-27T20:36:39.076449Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 57/256
|
|
||||||
[2m2026-04-27T20:36:39.078254Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 250/256
|
|
||||||
[2m2026-04-27T20:36:39.082390Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 251/256
|
|
||||||
[2m2026-04-27T20:36:39.082697Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 245/256
|
|
||||||
[2m2026-04-27T20:36:39.250465Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 50/256
|
|
||||||
[2m2026-04-27T20:36:39.448799Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 54/256
|
|
||||||
[2m2026-04-27T20:36:39.449166Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 62/256
|
|
||||||
[2m2026-04-27T20:36:39.450954Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 63/256
|
|
||||||
[2m2026-04-27T20:36:39.766480Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 253/256
|
|
||||||
[2m2026-04-27T20:36:39.838346Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 59/256
|
|
||||||
[2m2026-04-27T20:36:39.875987Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 255/256
|
|
||||||
[2m2026-04-27T20:36:39.876798Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 55/256
|
|
||||||
[2m2026-04-27T20:36:39.877292Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 51/256
|
|
||||||
[2m2026-04-27T20:36:40.244598Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 61/256
|
|
||||||
[2m2026-04-27T20:36:40.245589Z[0m [32m INFO[0m [2mobikpartitionner::partition[0m[2m:[0m counting kmers in partition 53/256
|
|
||||||
266.84 real 3776.35 user 115.80 sys
|
|
||||||
2423504896 maximum resident set size
|
|
||||||
0 average shared memory size
|
|
||||||
0 average unshared data size
|
|
||||||
0 average unshared stack size
|
|
||||||
292303 page reclaims
|
|
||||||
132311 page faults
|
|
||||||
0 swaps
|
|
||||||
0 block input operations
|
|
||||||
0 block output operations
|
|
||||||
0 messages sent
|
|
||||||
0 messages received
|
|
||||||
0 signals received
|
|
||||||
4462 voluntary context switches
|
|
||||||
1991864 involuntary context switches
|
|
||||||
54933227607056 instructions retired
|
|
||||||
11271230983971 cycles elapsed
|
|
||||||
2210777320 peak memory footprint
|
|
||||||
@@ -1 +0,0 @@
|
|||||||
(Escherichia_coli--CFT073:0.7973338454,(Escherichia_coli--EDL933:0.5132866305,(Escherichia_coli--K-12_MG1655:0.2990687226,Escherichia_coli--K-12_W3110:0.3006288477)100:0.1655629834)69:0.0000007189,(((Klebsiella_pneumoniae--ATCC_13883:0.9661675519,(Klebsiella_pneumoniae--MGH_78578:0.3148953385,Yersinia_ruckeri--YRB:0.3576917943)84:0.4568464394)83:0.0727808943,(Klebsiella_pneumoniae--HS11286:0.1397401144,Proteus_mirabilis--HI4320:0.2192824480)77:0.3686486712)76:0.1162295711,((Salmonella_enterica--AKU_12601:0.6158730439,(Salmonella_enterica--LT2:0.4371443730,Salmonella_enterica--P125109:0.5815549929)100:0.1012287522)100:0.0714169372,Salmonella_enterica--CT18:0.2058143021)76:0.3641489914)100:0.2900565429);
|
|
||||||
@@ -1,62 +0,0 @@
|
|||||||
#nexus
|
|
||||||
|
|
||||||
BEGIN Taxa;
|
|
||||||
DIMENSIONS ntax=13;
|
|
||||||
TAXLABELS
|
|
||||||
[1] 'Escherichia_coli--CFT073'
|
|
||||||
[2] 'Escherichia_coli--EDL933'
|
|
||||||
[3] 'Escherichia_coli--K-12_MG1655'
|
|
||||||
[4] 'Escherichia_coli--K-12_W3110'
|
|
||||||
[5] 'Klebsiella_pneumoniae--ATCC_13883'
|
|
||||||
[6] 'Klebsiella_pneumoniae--HS11286'
|
|
||||||
[7] 'Klebsiella_pneumoniae--MGH_78578'
|
|
||||||
[8] 'Proteus_mirabilis--HI4320'
|
|
||||||
[9] 'Salmonella_enterica--AKU_12601'
|
|
||||||
[10] 'Salmonella_enterica--CT18'
|
|
||||||
[11] 'Salmonella_enterica--LT2'
|
|
||||||
[12] 'Salmonella_enterica--P125109'
|
|
||||||
[13] 'Yersinia_ruckeri--YRB'
|
|
||||||
;
|
|
||||||
END; [Taxa]
|
|
||||||
|
|
||||||
BEGIN Splits;
|
|
||||||
DIMENSIONS ntax=13 nsplits=34;
|
|
||||||
FORMAT labels=no weights=yes confidences=no intervals=no;
|
|
||||||
MATRIX
|
|
||||||
100 2,
|
|
||||||
100 3,
|
|
||||||
100 4,
|
|
||||||
100 3 4,
|
|
||||||
69 2 3 4,
|
|
||||||
100 5,
|
|
||||||
100 7,
|
|
||||||
16 5 7,
|
|
||||||
100 6,
|
|
||||||
100 13,
|
|
||||||
16 6 13,
|
|
||||||
23 5 6 7 13,
|
|
||||||
100 8,
|
|
||||||
100 10,
|
|
||||||
23 8 10,
|
|
||||||
100 9,
|
|
||||||
100 11,
|
|
||||||
100 12,
|
|
||||||
100 11 12,
|
|
||||||
100 9 11 12,
|
|
||||||
23 8 9 10 11 12,
|
|
||||||
100 1 2 3 4,
|
|
||||||
100 1,
|
|
||||||
84 7 13,
|
|
||||||
83 5 7 13,
|
|
||||||
77 6 8,
|
|
||||||
76 5 6 7 8 13,
|
|
||||||
76 9 10 11 12,
|
|
||||||
31 1 2,
|
|
||||||
1 5 6 7 8,
|
|
||||||
1 10 13,
|
|
||||||
1 9 10 11 12 13,
|
|
||||||
1 5 6 13,
|
|
||||||
1 5 6 8,
|
|
||||||
;
|
|
||||||
END; [Splits]
|
|
||||||
|
|
||||||
-1000
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -1 +0,0 @@
|
|||||||
(((((((((((((Salmonella_enterica--P125109:0.009029074806027838,Salmonella_enterica--LT2:0.010374535686866677):0.00299392644685007,Salmonella_enterica--AKU_12601:0.010129090864056669):0.008889984754373365,Salmonella_enterica--CT18:0.029563522158784489):0.05178212639099835,(Escherichia_coli--CFT073:0.018265758526676266,(Escherichia_coli--EDL933:0.01586939152374907,(Escherichia_coli--K-12_MG1655:0.0043321525684933419,Escherichia_coli--K-12_W3110:0.004373581717010194):0.007835004272817602):0.005522415854494232):0.05395833543383322):0.007199364670842333,(Klebsiella_pneumoniae--HS11286:0.027306681424389149,(Klebsiella_pneumoniae--ATCC_13883:0.015176538442299506,Klebsiella_pneumoniae--MGH_78578:0.026462018414958045):0.0015885400482290244):0.060738462006352359):0.029481404183583916,Yersinia_ruckeri--YRB:0.10269826524749153):0.004316815340436764,Proteus_mirabilis--HI4320:0.11745645944715785):0.04439101156727093,Wolbachia_endosymbiont--GCF_000306885.1_ASM30688v1:0.17151356406519997):0.011344480816758762,Acidobacterium_capsulatum--ATCC_51196:0.17121217909071463):0.01869709592355495,Shouchella_clausii--KSM-K16:0.1554729916092201):0.04397682726757515,Bacillus_subtilis--168:0.10403127799132669):0.08828869671555731,Opitutus_terrae--PB90-1:0.06380512639846864):0.41655625366738377,Candidozyma_auris--GCF_003013715.1_ASM301371v2:0.22735026269091164,Saccharolobus_islandicus--M.16.4:0.21891918239548398);
|
|
||||||
Binary file not shown.
Binary file not shown.
@@ -1,167 +0,0 @@
|
|||||||
ratio_ceiling: 0.5
|
|
||||||
cardinality_transitions:
|
|
||||||
- from: 0
|
|
||||||
to: 0
|
|
||||||
count: 54999793
|
|
||||||
probability: 0.7934021725308564
|
|
||||||
- from: 0
|
|
||||||
to: 1
|
|
||||||
count: 8873859
|
|
||||||
probability: 0.12801028195383377
|
|
||||||
- from: 0
|
|
||||||
to: 2
|
|
||||||
count: 5305545
|
|
||||||
probability: 0.07653539585976665
|
|
||||||
- from: 0
|
|
||||||
to: 3
|
|
||||||
count: 126109
|
|
||||||
probability: 0.001819191475424167
|
|
||||||
- from: 0
|
|
||||||
to: 4
|
|
||||||
count: 16149
|
|
||||||
probability: 0.00023295818011898336
|
|
||||||
- from: 1
|
|
||||||
to: 0
|
|
||||||
count: 8873859
|
|
||||||
probability: 0.8510749571674425
|
|
||||||
- from: 1
|
|
||||||
to: 1
|
|
||||||
count: 1041044
|
|
||||||
probability: 0.09984455215137214
|
|
||||||
- from: 1
|
|
||||||
to: 2
|
|
||||||
count: 507272
|
|
||||||
probability: 0.048651493749477304
|
|
||||||
- from: 1
|
|
||||||
to: 3
|
|
||||||
count: 4248
|
|
||||||
probability: 0.00040741760918753563
|
|
||||||
- from: 1
|
|
||||||
to: 4
|
|
||||||
count: 225
|
|
||||||
probability: 0.00002157932252052625
|
|
||||||
- from: 2
|
|
||||||
to: 0
|
|
||||||
count: 5305545
|
|
||||||
probability: 0.9117891245815953
|
|
||||||
- from: 2
|
|
||||||
to: 1
|
|
||||||
count: 507272
|
|
||||||
probability: 0.08717767784549091
|
|
||||||
- from: 2
|
|
||||||
to: 2
|
|
||||||
count: 5227
|
|
||||||
probability: 0.0008982907041949506
|
|
||||||
- from: 2
|
|
||||||
to: 3
|
|
||||||
count: 689
|
|
||||||
probability: 0.00011840870388182915
|
|
||||||
- from: 2
|
|
||||||
to: 4
|
|
||||||
count: 96
|
|
||||||
probability: 0.000016498164836945715
|
|
||||||
- from: 3
|
|
||||||
to: 0
|
|
||||||
count: 126109
|
|
||||||
probability: 0.9614164824273843
|
|
||||||
- from: 3
|
|
||||||
to: 1
|
|
||||||
count: 4248
|
|
||||||
probability: 0.03238545399100404
|
|
||||||
- from: 3
|
|
||||||
to: 2
|
|
||||||
count: 689
|
|
||||||
probability: 0.005252725470763132
|
|
||||||
- from: 3
|
|
||||||
to: 3
|
|
||||||
count: 98
|
|
||||||
probability: 0.0007471220553480217
|
|
||||||
- from: 3
|
|
||||||
to: 4
|
|
||||||
count: 26
|
|
||||||
probability: 0.00019821605550049553
|
|
||||||
- from: 4
|
|
||||||
to: 0
|
|
||||||
count: 16149
|
|
||||||
probability: 0.9781344639612356
|
|
||||||
- from: 4
|
|
||||||
to: 1
|
|
||||||
count: 225
|
|
||||||
probability: 0.013628104179285281
|
|
||||||
- from: 4
|
|
||||||
to: 2
|
|
||||||
count: 96
|
|
||||||
probability: 0.00581465778316172
|
|
||||||
- from: 4
|
|
||||||
to: 3
|
|
||||||
count: 26
|
|
||||||
probability: 0.0015748031496062992
|
|
||||||
- from: 4
|
|
||||||
to: 4
|
|
||||||
count: 14
|
|
||||||
probability: 0.0008479709267110841
|
|
||||||
composition_transitions:
|
|
||||||
- from: 'A'
|
|
||||||
to: 'A'
|
|
||||||
count: 161774
|
|
||||||
probability: 0.4701762136303263
|
|
||||||
- from: 'A'
|
|
||||||
to: 'C'
|
|
||||||
count: 27788
|
|
||||||
probability: 0.0807624007835592
|
|
||||||
- from: 'A'
|
|
||||||
to: 'G'
|
|
||||||
count: 130019
|
|
||||||
probability: 0.3778842157577942
|
|
||||||
- from: 'A'
|
|
||||||
to: 'T'
|
|
||||||
count: 24490
|
|
||||||
probability: 0.07117716982832031
|
|
||||||
- from: 'C'
|
|
||||||
to: 'A'
|
|
||||||
count: 27788
|
|
||||||
probability: 0.0780165140757087
|
|
||||||
- from: 'C'
|
|
||||||
to: 'C'
|
|
||||||
count: 184047
|
|
||||||
probability: 0.5167232390273484
|
|
||||||
- from: 'C'
|
|
||||||
to: 'G'
|
|
||||||
count: 19622
|
|
||||||
probability: 0.05508996830263265
|
|
||||||
- from: 'C'
|
|
||||||
to: 'T'
|
|
||||||
count: 124724
|
|
||||||
probability: 0.3501702785943102
|
|
||||||
- from: 'G'
|
|
||||||
to: 'A'
|
|
||||||
count: 130019
|
|
||||||
probability: 0.3610094570655886
|
|
||||||
- from: 'G'
|
|
||||||
to: 'C'
|
|
||||||
count: 19622
|
|
||||||
probability: 0.05448224926003876
|
|
||||||
- from: 'G'
|
|
||||||
to: 'G'
|
|
||||||
count: 183951
|
|
||||||
probability: 0.5107565097152884
|
|
||||||
- from: 'G'
|
|
||||||
to: 'T'
|
|
||||||
count: 26562
|
|
||||||
probability: 0.07375178395908417
|
|
||||||
- from: 'T'
|
|
||||||
to: 'A'
|
|
||||||
count: 24490
|
|
||||||
probability: 0.07335783586895636
|
|
||||||
- from: 'T'
|
|
||||||
to: 'C'
|
|
||||||
count: 124724
|
|
||||||
probability: 0.37360076443118473
|
|
||||||
- from: 'T'
|
|
||||||
to: 'G'
|
|
||||||
count: 26562
|
|
||||||
probability: 0.07956434611479049
|
|
||||||
- from: 'T'
|
|
||||||
to: 'T'
|
|
||||||
count: 158067
|
|
||||||
probability: 0.4734770535850684
|
|
||||||
@@ -1,660 +0,0 @@
|
|||||||
<h1 id="obikmer">obikmer</h1>
|
|
||||||
<p><code>obikmer</code> is a Rust tool for manipulation, counting,
|
|
||||||
indexing, and set operations on DNA sequences represented as kmer
|
|
||||||
sets.</p>
|
|
||||||
<h2 id="constraints">Constraints</h2>
|
|
||||||
<ul>
|
|
||||||
<li>Target scale: metagenomic data, tens of Gbases, billions of
|
|
||||||
kmers</li>
|
|
||||||
<li>Maximum efficiency in computation, memory, and disk usage</li>
|
|
||||||
<li>k is odd, k ∈ [11, 31], fixed at runtime</li>
|
|
||||||
<li>Input formats: FASTA, FASTQ, gzip, streaming stdin</li>
|
|
||||||
</ul>
|
|
||||||
<h2 id="input-processing">Input processing</h2>
|
|
||||||
<p>For sequence files (FASTA/FASTQ):</p>
|
|
||||||
<ul>
|
|
||||||
<li>Cut sequence on non-ACGT nucleotides.</li>
|
|
||||||
<li>Discard fragments < k.</li>
|
|
||||||
<li>For sequences > 256 nt: cut at 256, start new with k-1 overlap
|
|
||||||
(preserves all kmers, no duplicates).</li>
|
|
||||||
</ul>
|
|
||||||
<h2 id="super-kmers">Super-kmers</h2>
|
|
||||||
<p>The fundamental stored unit is a <strong>canonical
|
|
||||||
super-kmer</strong>: a maximal run of consecutive kmers sharing the same
|
|
||||||
<strong>non-canonical</strong> (raw forward) minimizer, canonized at the
|
|
||||||
end.</p>
|
|
||||||
<h3 id="construction">Construction</h3>
|
|
||||||
<p>Super-kmers are built using the <strong>non-canonical
|
|
||||||
minimizer</strong> (minimum forward m-mer, no revcomp comparison). Two
|
|
||||||
consecutive kmers belong to the same super-kmer if and only if their raw
|
|
||||||
forward minimizer is identical.</p>
|
|
||||||
<p>At the end of each super-kmer, the minimizer is canonized:
|
|
||||||
<code>canonical(M) = min(M, revcomp(M))</code>.</p>
|
|
||||||
<ul>
|
|
||||||
<li>If <code>canonical(M) == M</code>: the super-kmer is already in
|
|
||||||
canonical orientation — keep as-is.</li>
|
|
||||||
<li>If <code>canonical(M) == revcomp(M)</code>: reverse-complement the
|
|
||||||
entire super-kmer (and its minimizer).</li>
|
|
||||||
</ul>
|
|
||||||
<p>The reverse-complement step does not cause any additional splitting —
|
|
||||||
it only flips the orientation.</p>
|
|
||||||
<h3 id="why-non-canonical-minimizer">Why non-canonical minimizer?</h3>
|
|
||||||
<p>Using the raw forward minimizer (rather than the canonical minimizer)
|
|
||||||
means fewer candidates are considered at each position → the minimizer
|
|
||||||
changes more often → super-kmers are <strong>shorter or equal</strong>,
|
|
||||||
never longer, compared to the canonical-minimizer definition.</p>
|
|
||||||
<p>The key benefit is at dereplication: a forward read and its
|
|
||||||
reverse-complement covering the same genomic region both produce the
|
|
||||||
<strong>same canonical super-kmer</strong> after the canonization step.
|
|
||||||
Under the canonical-minimizer definition, they would share the same
|
|
||||||
canonical minimizer but have different sequences (one being the revcomp
|
|
||||||
of the other) — they would not dereplicate. Here they do, giving a
|
|
||||||
compression factor of ~2× on paired or double-stranded data.</p>
|
|
||||||
<h3 id="length">Length</h3>
|
|
||||||
<p>For a random minimizer of length m over k-mers of length k, the
|
|
||||||
density of minimizer positions is approximately 2/(k−m+2) <span
|
|
||||||
class="citation" data-cites="Zheng2020-ji Golan2025-xf">[@Zheng2020-ji;
|
|
||||||
@Golan2025-xf]</span>, giving an expected super-kmer length of (k+m)/2
|
|
||||||
nucleotides. For k=31, m=13: expected ≈ 22 nt. In practice super-kmers
|
|
||||||
rarely exceed a few dozen nucleotides — the 256 nt cap is almost never
|
|
||||||
reached. When it is, the super-kmer is split at 256 nt with a k−1
|
|
||||||
overlap, preserving all kmers without duplication.</p>
|
|
||||||
<h2 id="binary-storage-format">Binary storage format</h2>
|
|
||||||
<p>Memory-mappable binary format for sequence collections: store
|
|
||||||
super-kmers end-to-end with u64-aligned headers (add padding if needed
|
|
||||||
for 8-byte alignment). Include index blocks every B super-kmers
|
|
||||||
(B=1000-10000) for fast jumping to position J (O(N/B + B) scan
|
|
||||||
vs. separate index O(1) direct access), where N is total super-kmers in
|
|
||||||
file. Represent header as union/struct for field access.</p>
|
|
||||||
<h2 id="partitioning-and-indexing-architecture">Partitioning and
|
|
||||||
indexing architecture</h2>
|
|
||||||
<p>The canonical minimizer of a super-kmer is hashed to produce a
|
|
||||||
<strong>p-bit routing value</strong> (p is a collection-level
|
|
||||||
parameter):</p>
|
|
||||||
<pre><code>canonical minimizer → hash(minimizer) → p-bit value → PART → partition directory</code></pre>
|
|
||||||
<p>PART is computed once at phase 1 to open the correct partition file,
|
|
||||||
then discarded. It is recomputed on the fly at query time. It is never
|
|
||||||
stored in the super-kmer header.</p>
|
|
||||||
<p>Each partition holds one BBHash instance (phase 6) that indexes kmers
|
|
||||||
as plain u64 values — the minimizer plays no role inside the
|
|
||||||
partition.</p>
|
|
||||||
<p>Properties: - <strong>2^p partitions</strong>: p freely tunable at
|
|
||||||
collection creation; not constrained to powers of 4 - <strong>Uniform
|
|
||||||
distribution</strong>: hashing the canonical minimizer corrects the
|
|
||||||
lexicographic bias inherent in minimizer selection <span
|
|
||||||
class="citation"
|
|
||||||
data-cites="Zheng2020-ji Zheng2021-cc Pan2024-hb Kille2023-px Golan2025-xf">[@Zheng2020-ji;
|
|
||||||
@Zheng2021-cc; @Pan2024-hb; @Kille2023-px; @Golan2025-xf]</span> - The
|
|
||||||
odd-length constraint on m only ensures canonical form correctness
|
|
||||||
during minimizer computation — it does not affect the partition
|
|
||||||
layout</p>
|
|
||||||
<p><strong>Entropy constraint:</strong> the canonical minimizer has 2m
|
|
||||||
bits of entropy. Requesting p bits from the hash requires 2m ≥ p,
|
|
||||||
i.e. <strong>p ≤ 2m</strong>:</p>
|
|
||||||
<table>
|
|
||||||
<thead>
|
|
||||||
<tr>
|
|
||||||
<th>m</th>
|
|
||||||
<th>p max</th>
|
|
||||||
<th>Partitions max</th>
|
|
||||||
</tr>
|
|
||||||
</thead>
|
|
||||||
<tbody>
|
|
||||||
<tr>
|
|
||||||
<td>9</td>
|
|
||||||
<td>2</td>
|
|
||||||
<td>4</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>11</td>
|
|
||||||
<td>6</td>
|
|
||||||
<td>64</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>13</td>
|
|
||||||
<td>10</td>
|
|
||||||
<td>1 024</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>15</td>
|
|
||||||
<td>14</td>
|
|
||||||
<td>16 384</td>
|
|
||||||
</tr>
|
|
||||||
</tbody>
|
|
||||||
</table>
|
|
||||||
<p>For the typical configuration k=31, m=13: up to 1 024 partitions.
|
|
||||||
Choosing p > 2m−16 is possible but produces artificially colliding
|
|
||||||
PART values with no gain in routing granularity.</p>
|
|
||||||
<h2 id="construction-pipeline">Construction pipeline</h2>
|
|
||||||
<p>All phases after scatter are embarrassingly parallel across
|
|
||||||
partitions.</p>
|
|
||||||
<h3 id="phase-1-scatter">Phase 1 — Scatter</h3>
|
|
||||||
<p>Single streaming pass over raw input files (FASTA/FASTQ, gzip). FASTQ
|
|
||||||
quality scores are ignored. For each read:</p>
|
|
||||||
<ol type="1">
|
|
||||||
<li><strong>Ambiguous base filter</strong>: cut at any non-ACGT base;
|
|
||||||
discard fragments shorter than k.</li>
|
|
||||||
<li><strong>Entropy filter</strong>: scan each fragment with a sliding
|
|
||||||
window of size k. When the kmer <span class="math inline">$K_i = S[i
|
|
||||||
\mathinner{..} i+k-1]$</span> ended by nucleotide <span
|
|
||||||
class="math inline"><em>S</em>[<em>j</em>]</span> (with <span
|
|
||||||
class="math inline"><em>j</em> = <em>i</em> + <em>k</em> − 1</span>) has
|
|
||||||
entropy below threshold <span class="math inline"><em>θ</em></span>,
|
|
||||||
emit the current segment and start a new one (see algorithm below).
|
|
||||||
<span class="math inline"><em>K</em><sub><em>i</em></sub></span> belongs
|
|
||||||
to neither segment, and no valid kmer is lost.</li>
|
|
||||||
<li><strong>Super-kmer extraction</strong>: for each clean segment,
|
|
||||||
slide a minimizer window and group consecutive kmers sharing the same
|
|
||||||
raw minimizer; canonise at the end.</li>
|
|
||||||
<li><strong>Partition routing</strong>:
|
|
||||||
<code>hash(canonical_minimizer) → PART</code> → append super-kmer to
|
|
||||||
<code>partition/superkmers.bin.gz</code>.</li>
|
|
||||||
</ol>
|
|
||||||
<p><strong>Entropy filter algorithm:</strong></p>
|
|
||||||
<p>When <span class="math inline"><em>K</em><sub><em>i</em></sub></span>
|
|
||||||
(ended by <span class="math inline"><em>S</em>[<em>j</em>]</span>, <span
|
|
||||||
class="math inline"><em>j</em> = <em>i</em> + <em>k</em> − 1</span>)
|
|
||||||
fails the entropy threshold:</p>
|
|
||||||
<ul>
|
|
||||||
<li>Current segment <span class="math inline">$S[\textit{seg_start}
|
|
||||||
\mathinner{..} j-1]$</span> is emitted (last valid kmer = <span
|
|
||||||
class="math inline"><em>K</em><sub><em>i</em> − 1</sub></span>)</li>
|
|
||||||
<li>New segment starts at <span
|
|
||||||
class="math inline"><em>S</em>[<em>i</em> + 1]</span> (first new kmer =
|
|
||||||
<span
|
|
||||||
class="math inline"><em>K</em><sub><em>i</em> + 1</sub></span>)</li>
|
|
||||||
<li><span class="math inline"><em>K</em><sub><em>i</em></sub></span> is
|
|
||||||
excluded: current segment lacks <span
|
|
||||||
class="math inline"><em>S</em>[<em>j</em>]</span>, new segment lacks
|
|
||||||
<span class="math inline"><em>S</em>[<em>i</em>]</span></li>
|
|
||||||
<li>Overlap = <span class="math inline">$S[i+1 \mathinner{..}
|
|
||||||
j-1]$</span> = <span class="math inline"><em>k</em> − 2</span>
|
|
||||||
nucleotides</li>
|
|
||||||
</ul>
|
|
||||||
<pre class="pseudocode"><code>\begin{algorithm}
|
|
||||||
\caption{Entropy filter — sliding window segmentation}
|
|
||||||
\begin{algorithmic}
|
|
||||||
\PROCEDURE{EntropyFilter}{S, N, k, theta}
|
|
||||||
\STATE seg_start <- 0
|
|
||||||
\STATE window <- []
|
|
||||||
\FOR{j <- 0 \TO N-1}
|
|
||||||
\STATE window.push(S[j])
|
|
||||||
\IF{|window| < k}
|
|
||||||
\STATE continue
|
|
||||||
\ENDIF
|
|
||||||
\STATE i <- j - k + 1
|
|
||||||
\IF{entropy(window) <= theta}
|
|
||||||
\STATE emit S[seg_start .. j-1]
|
|
||||||
\STATE seg_start <- i + 1
|
|
||||||
\STATE window <- S[i+1 .. j]
|
|
||||||
\ELSE
|
|
||||||
\STATE window.pop_front()
|
|
||||||
\ENDIF
|
|
||||||
\ENDFOR
|
|
||||||
\STATE emit S[seg_start .. N-1]
|
|
||||||
\ENDPROCEDURE
|
|
||||||
\end{algorithmic}
|
|
||||||
\end{algorithm}</code></pre>
|
|
||||||
<p>Writes are sequential and append-only — IO-friendly. Gzip applied at
|
|
||||||
write time. Data volume ≈ raw genome size (2 bits/nt compaction offsets
|
|
||||||
header overhead).</p>
|
|
||||||
<h3 id="phase-2-dereplication">Phase 2 — Dereplication</h3>
|
|
||||||
<p>Performed independently per partition. Identical super-kmers are
|
|
||||||
consolidated and their COUNT accumulated — analogous to amplicon
|
|
||||||
dereplication in metabarcoding. Uses external bucket sort to stay within
|
|
||||||
RAM bounds:</p>
|
|
||||||
<p><strong>Pass 1</strong> (streaming): hash the nucleotide payload of
|
|
||||||
each super-kmer, route to one of B bucket files:</p>
|
|
||||||
<pre><code>hash(sequence) % B → bucket_i.bin</code></pre>
|
|
||||||
<p>B ≈ 100 is tunable; RAM needed ≈ partition_size / B.</p>
|
|
||||||
<p><strong>Pass 2</strong>: for each bucket, load into an in-memory
|
|
||||||
<code>HashMap<sequence, COUNT></code>, dereplicate by summing
|
|
||||||
COUNT values, write consolidated super-kmers.</p>
|
|
||||||
<p>After dereplication: at Nx coverage the partition shrinks by ~x
|
|
||||||
(errors aside). The COUNT field in each super-kmer header = number of
|
|
||||||
times that exact super-kmer sequence was observed across all input
|
|
||||||
reads.</p>
|
|
||||||
<p><strong>Important:</strong> super-kmer COUNT ≠ individual kmer count.
|
|
||||||
A kmer can appear in multiple distinct super-kmers (same partition,
|
|
||||||
different flanking context); its true count = sum of COUNT of all
|
|
||||||
super-kmers containing it. A super-kmer with COUNT=1 may contain only
|
|
||||||
high-abundance kmers, each appearing in many other super-kmers.
|
|
||||||
Abundance filtering therefore cannot be applied at this phase.</p>
|
|
||||||
<h3 id="phase-3-per-kmer-count-aggregation-and-quorum-filtering">Phase 3
|
|
||||||
— Per-kmer count aggregation and quorum filtering</h3>
|
|
||||||
<p>For each dereplicated super-kmer, enumerate its kmers and accumulate
|
|
||||||
counts:</p>
|
|
||||||
<pre><code>for each super-kmer (sequence, COUNT):
|
|
||||||
for each kmer in sequence:
|
|
||||||
kmer_counts[canonical(kmer)] += COUNT</code></pre>
|
|
||||||
<p>Implemented as an external sort or a temporary HashMap, depending on
|
|
||||||
partition size. At the end of this phase, each distinct canonical kmer
|
|
||||||
has its exact total count.</p>
|
|
||||||
<p>Abundance filter applied here: kmers with
|
|
||||||
<code>total_count < q</code> are discarded. <code>q</code> is a
|
|
||||||
collection parameter (0 = keep all, including singletons for ≤1x
|
|
||||||
data).</p>
|
|
||||||
<p>No pre-filter on super-kmer COUNT is possible at phase 2: a
|
|
||||||
super-kmer with COUNT=1 may contain only high-abundance kmers, each
|
|
||||||
present in many other super-kmers across the partition.</p>
|
|
||||||
<h3 id="phase-4-super-kmer-compaction">Phase 4 — Super-kmer
|
|
||||||
compaction</h3>
|
|
||||||
<p>The valid kmer set from phase 3 is used as a mask to rewrite the
|
|
||||||
super-kmer files:</p>
|
|
||||||
<pre><code>for each dereplicated super-kmer:
|
|
||||||
scan kmer by kmer
|
|
||||||
kmer not in valid set → break point (terminates current super-kmer)
|
|
||||||
kmer in valid set → extend current super-kmer</code></pre>
|
|
||||||
<p>Three cases per super-kmer: - <strong>All kmers valid</strong> →
|
|
||||||
copied as-is - <strong>No kmer valid</strong> → discarded -
|
|
||||||
<strong>Mixed</strong> → split into sub-super-kmers at invalid
|
|
||||||
boundaries; each sub-super-kmer inherits the original COUNT</p>
|
|
||||||
<p>After splitting, re-apply dereplication (bucket sort, phase 2 method)
|
|
||||||
— splitting can produce new identical super-kmers. This re-dereplication
|
|
||||||
is cheap: the volume is already greatly reduced.</p>
|
|
||||||
<p>Output: a clean super-kmer file where every kmer passes quorum. This
|
|
||||||
file feeds phase 5.</p>
|
|
||||||
<h3 id="phase-5-local-de-bruijn-graph-and-unitig-construction">Phase 5 —
|
|
||||||
Local de Bruijn graph and unitig construction</h3>
|
|
||||||
<p>Within each partition, build a <strong>local de Bruijn graph</strong>
|
|
||||||
from the valid kmer set and compute its unitigs. All operations are
|
|
||||||
local to the partition — no cross-partition communication.</p>
|
|
||||||
<pre><code>valid kmers → HashSet<u64>
|
|
||||||
|
|
||||||
for each kmer K:
|
|
||||||
out_degree = |{K[1:]+b | b ∈ {A,C,G,T}} ∩ HashSet|
|
|
||||||
in_degree = |{b+K[:-1] | b ∈ {A,C,G,T}} ∩ HashSet|
|
|
||||||
|
|
||||||
internal node ↔ in_degree=1 AND out_degree=1
|
|
||||||
branching / dead-end → unitig start or end</code></pre>
|
|
||||||
<p>Traverse non-branching paths to assemble unitigs. Kmers whose
|
|
||||||
neighbours fall in other partitions appear as dead ends locally — they
|
|
||||||
terminate the unitig. The result: <strong>each kmer appears in exactly
|
|
||||||
one unitig</strong> within the partition.</p>
|
|
||||||
<p>The partition size (controlled by p) must be calibrated so that the
|
|
||||||
HashSet fits in RAM during this phase.</p>
|
|
||||||
<p>Output: <code>unitigs.bin</code> — the permanent evidence structure
|
|
||||||
for the partition. Each kmer in the partition appears at exactly one
|
|
||||||
(unitig_id, offset) location.</p>
|
|
||||||
<p><strong>Scope of local unitigs:</strong> these are unitigs of the
|
|
||||||
partition’s local de Bruijn graph, not global unitigs. A kmer whose k-1
|
|
||||||
successor or predecessor falls in another partition appears as a dead
|
|
||||||
end locally and terminates the unitig. This does not affect correctness
|
|
||||||
of verification but means partition-local unitigs cannot be directly
|
|
||||||
reused for global assembly.</p>
|
|
||||||
<h3 id="phase-6-bbhash-construction-and-index-finalisation">Phase 6 —
|
|
||||||
BBHash construction and index finalisation</h3>
|
|
||||||
<p>Built once on the definitive kmer set (all kmers in all unitigs of
|
|
||||||
the partition):</p>
|
|
||||||
<pre><code>kmers from unitigs → BBHash → bbhash.bin
|
|
||||||
→ counts.bin : packed n-bit array (or 1-bit for presence mode)
|
|
||||||
→ refs.bin : (unitig_id: u32, kmer_offset: u8) per kmer</code></pre>
|
|
||||||
<p>BBHash is built once — no rebuild. The n-bit width for
|
|
||||||
<code>counts.bin</code> is chosen from the observed count distribution
|
|
||||||
(n=5 covers ~97% of kmers at 15x; n=1 for presence mode). Counts
|
|
||||||
exceeding 2ⁿ−1 go into <code>overflow.bin</code> as sorted
|
|
||||||
<code>(bbhash_index: u32, count: u32)</code> pairs.</p>
|
|
||||||
<p><strong>Exact verification via unitig evidence:</strong></p>
|
|
||||||
<p><code>unitigs.bin</code> serves as the evidence structure: for any
|
|
||||||
query kmer, the stored unitig provides the ground truth to confirm or
|
|
||||||
deny its presence. BBHash maps every input to [0, N) including absent
|
|
||||||
kmers — the unitig read-back is the only way to guarantee exactness.</p>
|
|
||||||
<pre><code>query kmer q
|
|
||||||
→ minimizer(q) → hash → PART, KEY → partition
|
|
||||||
→ BBHash(q) → index i
|
|
||||||
→ refs[i] = (unitig_id, offset)
|
|
||||||
→ read unitig unitig_id from unitigs.bin
|
|
||||||
→ extract kmer at offset → compare with q
|
|
||||||
→ match : return counts[i] ← exact hit
|
|
||||||
→ no match: kmer absent ← BBHash collision on absent kmer</code></pre>
|
|
||||||
<p>One random disk access into <code>unitigs.bin</code> per query; the
|
|
||||||
unitig is the minimal, non-redundant evidence (each kmer stored
|
|
||||||
once).</p>
|
|
||||||
<h2 id="on-disk-collection-structure">On-disk collection structure</h2>
|
|
||||||
<p>Collections are too large to hold in RAM (hundreds of genomes,
|
|
||||||
billions of kmers). The collection lives on disk as a directory of
|
|
||||||
memory-mapped files:</p>
|
|
||||||
<pre><code>collection/
|
|
||||||
metadata.toml — collection parameters (see below)
|
|
||||||
superkmers.bin — super-kmer sequences, end-to-end, memory-mappable
|
|
||||||
superkmers.idx — index blocks every B super-kmers for fast seeking
|
|
||||||
part_XXXX/
|
|
||||||
bbhash.bin — BBHash function for this partition
|
|
||||||
counts.bin — packed n-bit count array (or 1-bit presence array)
|
|
||||||
refs.bin — back-references for exact verification</code></pre>
|
|
||||||
<p><strong>Collection parameters</strong> (stored in
|
|
||||||
<code>metadata.toml</code>):</p>
|
|
||||||
<table>
|
|
||||||
<thead>
|
|
||||||
<tr>
|
|
||||||
<th>Parameter</th>
|
|
||||||
<th>Role</th>
|
|
||||||
</tr>
|
|
||||||
</thead>
|
|
||||||
<tbody>
|
|
||||||
<tr>
|
|
||||||
<td>k</td>
|
|
||||||
<td>kmer length</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>m</td>
|
|
||||||
<td>minimizer length (odd, < k)</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>p</td>
|
|
||||||
<td>partition bits (0 ≤ p ≤ min(14, 2m−16))</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>mode</td>
|
|
||||||
<td><code>presence</code> (1 bit/kmer) or <code>count</code> (n
|
|
||||||
bits/kmer)</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>n</td>
|
|
||||||
<td>bits per kmer in count mode (chosen at construction)</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>min_count</td>
|
|
||||||
<td>singleton filtering threshold (0 = keep all)</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>hash_fn</td>
|
|
||||||
<td>hash function identifier</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>hash_seed</td>
|
|
||||||
<td>seed for the hash function</td>
|
|
||||||
</tr>
|
|
||||||
</tbody>
|
|
||||||
</table>
|
|
||||||
<p><strong>Exact verification via back-reference:</strong></p>
|
|
||||||
<p>BBHash maps any input to [0, N) — including absent kmers. To avoid
|
|
||||||
false positives, <code>refs.bin</code> stores at each BBHash index a
|
|
||||||
back-reference <code>(superkmer_id: u32, kmer_offset: u8)</code> = 5
|
|
||||||
bytes. Query protocol:</p>
|
|
||||||
<pre><code>query kmer q
|
|
||||||
→ minimizer(q) → hash → PART, KEY → partition
|
|
||||||
→ BBHash(q) → index i
|
|
||||||
→ refs[i] = (sk_id, offset)
|
|
||||||
→ read super-kmer sk_id from superkmers.bin
|
|
||||||
→ extract kmer at offset → compare with q
|
|
||||||
→ if match: return counts[i] (exact)
|
|
||||||
→ if no match: kmer absent</code></pre>
|
|
||||||
<p><strong>Count storage — two modes:</strong></p>
|
|
||||||
<p><em>Presence mode</em> (coverage ≤ 1x, or when only presence/absence
|
|
||||||
matters): - <code>counts.bin</code> is a packed 1-bit array — all bits
|
|
||||||
set to 1 for indexed kmers - Singletons are the signal, not filtered</p>
|
|
||||||
<p><em>Count mode</em> (coverage > 1x): - <code>counts.bin</code> is
|
|
||||||
a packed n-bit array; n chosen at construction from the observed
|
|
||||||
distribution - Value 0: absent sentinel; values 1..2ⁿ−2: direct count;
|
|
||||||
value 2ⁿ−1: overflow - Overflow counts stored in a separate
|
|
||||||
<code>overflow.bin</code> as sorted
|
|
||||||
<code>(index: u32, count: u32)</code> pairs - Empirically (k=31, 15x
|
|
||||||
coverage): n=5 covers 97% of real kmers, n=6 covers 99% - min_count
|
|
||||||
threshold filters low-frequency kmers (errors) before indexing; for ≤1x,
|
|
||||||
min_count=0</p>
|
|
||||||
<p><strong>BBHash:</strong> operates on kmer u64 values directly within
|
|
||||||
each partition. The minimizer plays no role inside the partition —
|
|
||||||
BBHash receives the kmer and builds the perfect hash naturally.</p>
|
|
||||||
<h2 id="kmer-entropy-filter">Kmer entropy filter</h2>
|
|
||||||
<p>Low-complexity kmers (polyA, polyT, tandem repeats) are detected and
|
|
||||||
excluded during phase 1. The filter computes a <strong>normalized
|
|
||||||
Shannon entropy</strong> over sub-words of multiple sizes, corrected for
|
|
||||||
two sources of bias: the small number of observations within a single
|
|
||||||
kmer, and the unequal sizes of circular equivalence classes.</p>
|
|
||||||
<h3 id="sub-word-frequencies">Sub-word frequencies</h3>
|
|
||||||
<p>For a kmer of length k and a sub-word size ws (1 ≤ ws ≤ ws_max,
|
|
||||||
typically ws_max = 6), extract the <span
|
|
||||||
class="math inline"><em>n</em><sub>words</sub> = <em>k</em> − <em>w</em><em>s</em> + 1</span>
|
|
||||||
overlapping sub-words by sliding a window of length ws:</p>
|
|
||||||
<p><span class="math display">$$w_i = \text{kmer}[i \mathinner{..}
|
|
||||||
i+ws-1], \quad i = 0, \ldots, n_{\text{words}}-1$$</span></p>
|
|
||||||
<p>Each sub-word is mapped to its <strong>circular canonical
|
|
||||||
form</strong>: the lexicographic minimum among all cyclic rotations of
|
|
||||||
the word. Let <span
|
|
||||||
class="math inline"><em>s</em><sub><em>j</em></sub></span> be the size
|
|
||||||
of equivalence class <span class="math inline"><em>j</em></span> (number
|
|
||||||
of distinct raw words mapping to canonical form <span
|
|
||||||
class="math inline"><em>j</em></span>), and <span
|
|
||||||
class="math inline"><em>f</em><sub><em>j</em></sub></span> the count of
|
|
||||||
canonical form <span class="math inline"><em>j</em></span> among the
|
|
||||||
<span class="math inline"><em>n</em><sub>words</sub></span> sub-words
|
|
||||||
(<span
|
|
||||||
class="math inline">∑<sub><em>j</em></sub><em>f</em><sub><em>j</em></sub> = <em>n</em><sub>words</sub></span>).</p>
|
|
||||||
<h3 id="corrected-shannon-entropy">Corrected Shannon entropy</h3>
|
|
||||||
<p>The circular equivalence classes have unequal sizes: under a uniform
|
|
||||||
distribution over all <span
|
|
||||||
class="math inline">4<sup><em>w</em><em>s</em></sup></span> raw words,
|
|
||||||
class <span class="math inline"><em>j</em></span> is visited with
|
|
||||||
probability <span
|
|
||||||
class="math inline"><em>s</em><sub><em>j</em></sub>/4<sup><em>w</em><em>s</em></sup></span>,
|
|
||||||
not <span class="math inline">1/<em>n</em><sub><em>a</em></sub></span>.
|
|
||||||
Computing entropy directly over canonical classes therefore
|
|
||||||
underestimates the entropy of a random sequence.</p>
|
|
||||||
<p>The correction “unfolds” each canonical class back to its member raw
|
|
||||||
words, redistributing each observation of class <span
|
|
||||||
class="math inline"><em>j</em></span> equally among its <span
|
|
||||||
class="math inline"><em>s</em><sub><em>j</em></sub></span> members:</p>
|
|
||||||
<p><span class="math display">$$H_{\text{corr}} = \log(n_{\text{words}})
|
|
||||||
- \frac{1}{n_{\text{words}}} \sum_j f_j \log f_j +
|
|
||||||
\frac{1}{n_{\text{words}}} \sum_j f_j \log s_j$$</span></p>
|
|
||||||
<p>The last term is the correction for unequal class sizes. For a
|
|
||||||
uniformly random sequence (<span
|
|
||||||
class="math inline"><em>f</em><sub><em>j</em></sub> ≈ <em>n</em><sub>words</sub> ⋅ <em>s</em><sub><em>j</em></sub>/4<sup><em>w</em><em>s</em></sup></span>),
|
|
||||||
this gives <span
|
|
||||||
class="math inline"><em>H</em><sub>corr</sub> ≈ log (4<sup><em>w</em><em>s</em></sup>) = 2 ⋅ <em>w</em><em>s</em> ⋅ log 2</span>,
|
|
||||||
the maximum entropy over raw words.</p>
|
|
||||||
<h3 id="maximum-entropy-correction-for-small-samples">Maximum entropy
|
|
||||||
correction for small samples</h3>
|
|
||||||
<p>With only <span class="math inline"><em>n</em><sub>words</sub></span>
|
|
||||||
observations over <span
|
|
||||||
class="math inline">4<sup><em>w</em><em>s</em></sup></span> possible raw
|
|
||||||
words, the achievable maximum entropy is bounded by the most uniform
|
|
||||||
integer distribution over <span
|
|
||||||
class="math inline">4<sup><em>w</em><em>s</em></sup></span>
|
|
||||||
categories.</p>
|
|
||||||
<p>Let <span
|
|
||||||
class="math inline"><em>c</em> = ⌊<em>n</em><sub>words</sub>/4<sup><em>w</em><em>s</em></sup>⌋</span>
|
|
||||||
and <span
|
|
||||||
class="math inline"><em>r</em> = <em>n</em><sub>words</sub> mod 4<sup><em>w</em><em>s</em></sup></span>.
|
|
||||||
The most uniform integer distribution assigns frequency <span
|
|
||||||
class="math inline"><em>c</em> + 1</span> to <span
|
|
||||||
class="math inline"><em>r</em></span> categories and <span
|
|
||||||
class="math inline"><em>c</em></span> to the remaining <span
|
|
||||||
class="math inline">4<sup><em>w</em><em>s</em></sup> − <em>r</em></span>,
|
|
||||||
with the convention <span class="math inline">0log 0 = 0</span>:</p>
|
|
||||||
<p><span class="math display">$$H_{\max} = -\left[(4^{ws} -
|
|
||||||
r)\,\frac{c}{n_{\text{words}}}\log\frac{c}{n_{\text{words}}} +
|
|
||||||
r\,\frac{c+1}{n_{\text{words}}}\log\frac{c+1}{n_{\text{words}}}\right]$$</span></p>
|
|
||||||
<p>When <span
|
|
||||||
class="math inline"><em>n</em><sub>words</sub> < 4<sup><em>w</em><em>s</em></sup></span>:
|
|
||||||
<span class="math inline"><em>c</em> = 0</span>, <span
|
|
||||||
class="math inline"><em>r</em> = <em>n</em><sub>words</sub></span>, and
|
|
||||||
the formula reduces to <span
|
|
||||||
class="math inline"><em>H</em><sub>max</sub> = log (<em>n</em><sub>words</sub>)</span>
|
|
||||||
— a single unified expression covers both regimes. A truly random
|
|
||||||
sequence achieves <span
|
|
||||||
class="math inline"><em>H</em><sub>corr</sub> ≈ <em>H</em><sub>max</sub></span>.</p>
|
|
||||||
<h3 id="normalized-entropy">Normalized entropy</h3>
|
|
||||||
<p><span class="math display">$$\hat{H}(ws) =
|
|
||||||
\frac{H_{\text{corr}}}{H_{\max}} \in [0, 1]$$</span></p>
|
|
||||||
<h3 id="final-score">Final score</h3>
|
|
||||||
<p>The filter computes <span
|
|
||||||
class="math inline"><em>Ĥ</em>(<em>w</em><em>s</em>)</span> for each
|
|
||||||
word size ws from 1 to ws_max and returns the
|
|
||||||
<strong>minimum</strong>:</p>
|
|
||||||
<p><span class="math display">$$\text{entropy}(kmer) =
|
|
||||||
\min_{ws=1}^{ws_{\max}} \hat{H}(ws)$$</span></p>
|
|
||||||
<p>A value near 0 indicates low complexity (e.g. AAAA…); near 1
|
|
||||||
indicates high complexity. A kmer is rejected if <span
|
|
||||||
class="math inline">entropy(<em>k</em><em>m</em><em>e</em><em>r</em>) ≤ <em>θ</em></span>,
|
|
||||||
where <span class="math inline"><em>θ</em></span> is a collection
|
|
||||||
parameter. The minimum across word sizes ensures that any scale of
|
|
||||||
repetition is detected independently: polyA is caught at ws=1,
|
|
||||||
dinucleotide repeats at ws=2, etc.</p>
|
|
||||||
<h2 id="priority-operations">Priority operations</h2>
|
|
||||||
<ul>
|
|
||||||
<li>Kmer counting (frequencies)</li>
|
|
||||||
<li>Fast search / query</li>
|
|
||||||
<li>Set operations: union, intersection, difference</li>
|
|
||||||
</ul>
|
|
||||||
<h2 id="data-types">Data types</h2>
|
|
||||||
<p>Two types of DNA are represented:</p>
|
|
||||||
<ul>
|
|
||||||
<li><strong>Super-kmers</strong>: stored as a nucleotide sequence (2
|
|
||||||
bits/base, byte-aligned, no padding). Max length: 256 nucleotides (512
|
|
||||||
bits, 64 bytes). Each super-kmer has a <strong>32-bit
|
|
||||||
header</strong>:</li>
|
|
||||||
</ul>
|
|
||||||
<table>
|
|
||||||
<thead>
|
|
||||||
<tr>
|
|
||||||
<th>Field</th>
|
|
||||||
<th>Bits</th>
|
|
||||||
<th>Role</th>
|
|
||||||
</tr>
|
|
||||||
</thead>
|
|
||||||
<tbody>
|
|
||||||
<tr>
|
|
||||||
<td>COUNT</td>
|
|
||||||
<td>24</td>
|
|
||||||
<td>Occurrence count (≤ 16 M)</td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>SEQL</td>
|
|
||||||
<td>8</td>
|
|
||||||
<td>Sequence length in nucleotides (≤ 256)</td>
|
|
||||||
</tr>
|
|
||||||
</tbody>
|
|
||||||
</table>
|
|
||||||
<p>Bit layout (MSB to LSB):</p>
|
|
||||||
<pre><code>[31:8] COUNT [7:0] SEQL</code></pre>
|
|
||||||
<p>Getters:</p>
|
|
||||||
<div class="sourceCode" id="cb12"><pre
|
|
||||||
class="sourceCode rust"><code class="sourceCode rust"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="kw">fn</span> seql(<span class="op">&</span><span class="kw">self</span>) <span class="op">-></span> <span class="dt">u8</span> <span class="op">{</span> <span class="kw">self</span><span class="op">.</span><span class="dv">0</span> <span class="kw">as</span> <span class="dt">u8</span> <span class="op">}</span></span>
|
|
||||||
<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a><span class="kw">fn</span> count(<span class="op">&</span><span class="kw">self</span>) <span class="op">-></span> <span class="dt">u32</span> <span class="op">{</span> <span class="kw">self</span><span class="op">.</span><span class="dv">0</span> <span class="op">>></span> <span class="dv">8</span> <span class="op">}</span></span>
|
|
||||||
<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a><span class="kw">fn</span> increment(<span class="op">&</span><span class="kw">mut</span> <span class="kw">self</span>) <span class="op">{</span> <span class="kw">self</span><span class="op">.</span><span class="dv">0</span> <span class="op">+=</span> <span class="dv">1</span> <span class="op"><<</span> <span class="dv">8</span><span class="op">;</span> <span class="op">}</span></span></code></pre></div>
|
|
||||||
<p>PART and KEY were considered as routing fields derived from
|
|
||||||
<code>hash(minimizer)</code> but are single-use at phase 1 only —
|
|
||||||
neither is stored. The nucleotide sequence is always byte-aligned (no
|
|
||||||
offset): after reverse-complementing a super-kmer, a single bit-shift
|
|
||||||
realigns the sequence so that nucleotide 0 always starts at bit 0 of
|
|
||||||
word[0]. This shift is paid once at canonisation (phase 1, at most half
|
|
||||||
of super-kmers) and eliminates any need for an alignment offset field.
|
|
||||||
The direct consequence for dereplication: the byte array can be hashed
|
|
||||||
directly without any offset adjustment.</p>
|
|
||||||
<p>Note: minimizer selection (window minimum) biases the raw minimizer
|
|
||||||
distribution toward lexicographically small values <span
|
|
||||||
class="citation"
|
|
||||||
data-cites="Zheng2020-ji Zheng2021-cc Pan2024-hb Kille2023-px Golan2025-xf">[@Zheng2020-ji;
|
|
||||||
@Zheng2021-cc; @Pan2024-hb; @Kille2023-px; @Golan2025-xf]</span>;
|
|
||||||
hashing corrects this before partition routing.</p>
|
|
||||||
<ul>
|
|
||||||
<li><strong>Kmers</strong>: short DNA subsequences (k bases),
|
|
||||||
represented in <code>u64</code>.</li>
|
|
||||||
</ul>
|
|
||||||
<h2 id="kmer-representation">Kmer representation</h2>
|
|
||||||
<p>Each base is encoded on 2 bits, so any kmer with k ≤ 31 fits in a
|
|
||||||
<code>u64</code>.</p>
|
|
||||||
<h3 id="bit-layout">Bit layout</h3>
|
|
||||||
<p>Nucleotide <code>i</code> occupies bits <code>64-i</code> and
|
|
||||||
<code>63-i</code>. For a kmer of length k, 2k bits are used; the
|
|
||||||
low-order 64 - 2k bits of the u64 are kept at 0 and have no meaning.</p>
|
|
||||||
<ul>
|
|
||||||
<li>Extraction of nuc[i]:
|
|
||||||
<code>(word >> (63 - 2*i)) & 0b11</code>.</li>
|
|
||||||
</ul>
|
|
||||||
<p>For kmers (k ≤ 31), the whole sequence fits in a single
|
|
||||||
<code>u64</code>. For longer sequences up to 256 nucleotides (512 bits),
|
|
||||||
the representation extends across multiple words.</p>
|
|
||||||
<h3 id="complement-and-reverse-complement">Complement and reverse
|
|
||||||
complement</h3>
|
|
||||||
<p>The encoding is chosen so that the Watson-Crick complement of any
|
|
||||||
base is its bitwise NOT (on 2 bits):</p>
|
|
||||||
<table>
|
|
||||||
<thead>
|
|
||||||
<tr>
|
|
||||||
<th>Base</th>
|
|
||||||
<th>Encoding</th>
|
|
||||||
<th>Complement</th>
|
|
||||||
<th>NOT</th>
|
|
||||||
</tr>
|
|
||||||
</thead>
|
|
||||||
<tbody>
|
|
||||||
<tr>
|
|
||||||
<td>A</td>
|
|
||||||
<td><code>00</code></td>
|
|
||||||
<td>T</td>
|
|
||||||
<td><code>11</code></td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>C</td>
|
|
||||||
<td><code>01</code></td>
|
|
||||||
<td>G</td>
|
|
||||||
<td><code>10</code></td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>G</td>
|
|
||||||
<td><code>10</code></td>
|
|
||||||
<td>C</td>
|
|
||||||
<td><code>01</code></td>
|
|
||||||
</tr>
|
|
||||||
<tr>
|
|
||||||
<td>T</td>
|
|
||||||
<td><code>11</code></td>
|
|
||||||
<td>A</td>
|
|
||||||
<td><code>00</code></td>
|
|
||||||
</tr>
|
|
||||||
</tbody>
|
|
||||||
</table>
|
|
||||||
<p>This means <code>complement(base) = ~base & 0b11</code>, and the
|
|
||||||
reverse complement of a kmer reduces to two cheap operations:</p>
|
|
||||||
<pre><code>revcomp(kmer) = reverse_bases(~kmer & mask_2k)</code></pre>
|
|
||||||
<p>where <code>mask_2k = (1 << 2k) - 1</code> zeros the unused
|
|
||||||
high bits, and <code>reverse_bases</code> reorders the 2-bit chunks from
|
|
||||||
LSB to MSB. No lookup table needed.</p>
|
|
||||||
<p>DNA being double-stranded, each kmer and its reverse complement are
|
|
||||||
equivalent. The canonical form is defined as:</p>
|
|
||||||
<pre><code>canonical(kmer) = min(kmer, revcomp(kmer))</code></pre>
|
|
||||||
<p>This halves the kmer space and ensures strand-independent
|
|
||||||
counting.</p>
|
|
||||||
<h2 id="sequence-operations">Sequence operations</h2>
|
|
||||||
<h3 id="reverse-complement">Reverse complement</h3>
|
|
||||||
<p>Reverse complement of a super-kmer sequence (used at most once per
|
|
||||||
super-kmer, during phase 1 canonisation):</p>
|
|
||||||
<ol type="1">
|
|
||||||
<li>Reverse byte order</li>
|
|
||||||
<li>Apply 256-entry lookup table (precomputed reverse-complemented
|
|
||||||
bytes) to each byte</li>
|
|
||||||
<li>Bit-shift the result to realign nucleotide 0 to bit 0 of
|
|
||||||
word[0]</li>
|
|
||||||
</ol>
|
|
||||||
<p>The shift amount depends only on the sequence length:
|
|
||||||
<code>shift = (len % 4) * 2</code> bits. After the shift, the sequence
|
|
||||||
is byte-aligned with no offset — the same invariant as the original.</p>
|
|
||||||
<div class="sourceCode" id="cb15"><pre
|
|
||||||
class="sourceCode rust"><code class="sourceCode rust"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="kw">fn</span> reverse_complement(words<span class="op">:</span> <span class="op">&</span>[<span class="dt">u64</span>]<span class="op">,</span> len<span class="op">:</span> <span class="dt">usize</span>) <span class="op">-></span> <span class="dt">Vec</span><span class="op"><</span><span class="dt">u64</span><span class="op">></span> <span class="op">{</span></span>
|
|
||||||
<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a> <span class="kw">let</span> bytes <span class="op">=</span> words_to_bytes(words)<span class="op">;</span></span>
|
|
||||||
<span id="cb15-3"><a href="#cb15-3" aria-hidden="true" tabindex="-1"></a> <span class="kw">let</span> <span class="kw">mut</span> rev<span class="op">:</span> <span class="dt">Vec</span><span class="op"><</span><span class="dt">u8</span><span class="op">></span> <span class="op">=</span> bytes<span class="op">.</span>iter()<span class="op">.</span>rev()<span class="op">.</span>map(<span class="op">|&</span>b<span class="op">|</span> LOOKUP_TABLE[b <span class="kw">as</span> <span class="dt">usize</span>])<span class="op">.</span>collect()<span class="op">;</span></span>
|
|
||||||
<span id="cb15-4"><a href="#cb15-4" aria-hidden="true" tabindex="-1"></a> <span class="kw">let</span> shift <span class="op">=</span> (len <span class="op">%</span> <span class="dv">4</span>) <span class="op">*</span> <span class="dv">2</span><span class="op">;</span></span>
|
|
||||||
<span id="cb15-5"><a href="#cb15-5" aria-hidden="true" tabindex="-1"></a> <span class="cf">if</span> shift <span class="op">></span> <span class="dv">0</span> <span class="op">{</span> bit_shift_left(<span class="op">&</span><span class="kw">mut</span> rev<span class="op">,</span> shift)<span class="op">;</span> <span class="op">}</span></span>
|
|
||||||
<span id="cb15-6"><a href="#cb15-6" aria-hidden="true" tabindex="-1"></a> bytes_to_words(rev)</span>
|
|
||||||
<span id="cb15-7"><a href="#cb15-7" aria-hidden="true" tabindex="-1"></a><span class="op">}</span></span></code></pre></div>
|
|
||||||
<h2 id="multithreading">Multithreading</h2>
|
|
||||||
<p>For HPC with 100+ cores: use Rayon for data parallelism (parallel
|
|
||||||
iterators), std::thread for custom threading, or async with Tokio for
|
|
||||||
I/O-bound tasks. Equivalent to Go’s goroutines but with
|
|
||||||
ownership/borrowing safety.</p>
|
|
||||||
<p>Rayon: Rust crate for automatic data parallelism. Provides parallel
|
|
||||||
iterators (par_iter) that distribute work across CPU cores, e.g.,
|
|
||||||
vec.par_iter().map(|x| x*2).collect(). Handles thread
|
|
||||||
spawning/synchronization transparently. Widely used and maintained by
|
|
||||||
the Rust project. Orthogonal to Tokio (async runtime): Rayon for CPU
|
|
||||||
parallelism, Tokio for async I/O.</p>
|
|
||||||
<p>Data pipelines: use Crossbeam channels (MPMC) with threads/async,
|
|
||||||
equivalent to Go’s channels + goroutines.</p>
|
|
||||||
<p>Channels: std::sync::mpsc (built-in, MPSC, simple); crossbeam (crate,
|
|
||||||
MPMC, faster, more features like select). Use Crossbeam for
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multi-producer/multi-consumer scenarios.</p>
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<h1 id="bibliographie">Bibliographie</h1>
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<p>\bibliography</p>
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Reference in New Issue
Block a user