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Hi, I am trying out kat, but I do not get a genome estimation result:
I am running: kat hist -m 21 -h 200 -t 38 -v -p png -o wGorVio_kat wGorVio_reads.jf
Here is the log file output:
Kmer Analysis Toolkit (KAT) V2.4.2
Running KAT in HIST mode
------------------------
Loading hashes into memory... done. Time taken: 356.4s
Bining kmers ... done. Time taken: 3.4s
Merging counts ... done. Time taken: 0.0s
Saving results to disk ... done. Time taken: 0.0s
Creating plot ...
Plotting histograms for: 1
201 element histogram file loaded.
Axis limits:
xmax: 201
ymax: 5188216.0
done. Time taken: 2.9s
Analysing peaks
---------------
Analysing distributions for: /lustre/projects/dazzlerAssembly/asm_wGorVio/hifi/qc/reads/kat/wGorVio_kat
Input file generated using K 21
Kmer coverage histogram file detected
Analysing spectra
Creating initial peaks ... done. 1 peaks initially created
Index Left Mean Right StdDev Max Volume Description
------- ------ ------ ------- -------- ------- -------- -------------
1 80 100 120 10 1421407 0 1/2X
Locally optimising each peak ... done.
Index Left Mean Right StdDev Max Volume Description
------- ------ ------ ------- -------- ------- --------- -------------
1 24.02 99 173.98 37.49 1421406 132588455 1/2X
Fitting cumulative distribution to histogram by adjusting peaks ... done.
Index Left Mean Right StdDev Max Volume Description
------- ------ ------ ------- -------- ------- --------- -------------
1 10.78 98 185.22 43.61 1421406 152072606 1/2X
Time taken: 0.2s
K-mer frequency spectra statistics
----------------------------------
K-value used: 21
Peaks in analysis: 1
Global minima @ Frequency=12x (490472)
Global maxima @ Frequency=200x (6033723)
Overall mean k-mer frequency: 98x
Index Left Mean Right StdDev Max Volume Description
------- ------ ------ ------- -------- ------- --------- -------------
1 10.78 98 185.22 43.61 1421406 152072606 1/2X
Calculating genome statistics
-----------------------------
Assuming that homozygous peak is the largest in the spectra with frequency of: 98x
Homozygous peak index: 0
CAUTION: the following estimates are based on having a clean spectra and having identified the correct homozygous peak!
Estimated genome size: 0.00 Mbp
Creating plots
--------------
Plotting K-mer frequency distributions ... done. Saved to: None
KAT HIST completed.
Total runtime: 364.3s
alright, I figured out that it is my setting of the -h parameter, which screws with the calculation of the genome size / heterozygosity. when I leave this parameter out, both are calculated without hitch (although the graph is prettier with ;)
Hi, I am trying out kat, but I do not get a genome estimation result:
I am running:
kat hist -m 21 -h 200 -t 38 -v -p png -o wGorVio_kat wGorVio_reads.jf
Here is the log file output:
my results are:
Why are the estimated genome size and the estimated het rate zero?
I though the histogram was looking fine
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