Hi folks. I am trying to use your software KmerGenie. I have some problems. Because it does not draw the histograms at >15 value. It is hilarious when i put without diploid command. It could tell me the best k but without doing at >15. I tried from 15 to 55 because at more k (to121K) it is more slower (1h30min) at the result is the same "could not fit".
sudo ./kmergenie /home/soba/out_WGS_k25_quitado.fasta diploid l 15 k 55 o prueba
running histogram estimation
Linear estimation: ~15 M distinct 38mers are in the reads
Kmer sampling: 1/2

processing 
[going to estimate histograms for values of k: 55 45 35 25 15
Total time Wallclock 34.736 s
fitting model to histograms to estimate best k
could not fit pruebak15.histo
could not fit pruebak35.histo
could not fit pruebak25.histo
could not fit pruebak55.histo
could not fit pruebak45.histo
could not predict a best k value
Execution of decide failed (return code 0)
sudo ./kmergenie /home/soba/Documentos/out_WGS_k25_quitado.fasta l 15 k 55 o prueba
running histogram estimation
Linear estimation: ~15 M distinct 38mers are in the reads
Kmer sampling: 1/2
 processing 
[going to estimate histograms for values of k: 55 45 35 25 15
Total time Wallclock 35.6302 s
fitting model to histograms to estimate best k
could not fit pruebak25.histo
could not fit pruebak35.histo
could not fit pruebak45.histo
could not fit pruebak55.histo
estimation of the best k so far: 15
refining estimation around [15; 21], with a step of 2
running histogram estimation
Linear estimation: ~19 M distinct 21mers are in the reads
Kmer sampling: 1/3
 processing 
[going to estimate histograms for values of k: 21 19 17 15
Total time Wallclock 22.5893 s
fitting model to histograms to estimate best k
could not fit pruebak19.histo
could not fit pruebak17.histo
could not fit pruebak21.histo
could not fit pruebak25.histo
could not fit pruebak45.histo
could not fit pruebak35.histo
could not fit pruebak55.histo
table of predicted num. of genomic kmers: prueba.dat
recommended coverage cutoff for best k: 18
best k: 15
Just a note: try not to run programs as root (e.g. do not use sudo).
Ok. Now it showed the line was failed.
this one is due to a failure to overwrite the (possibly root) file prueba_report.html
It is me, the same. So, May it be a problem with R program? What are the correct installed packages?
Thanks for reporting this issue. Could you please send the
prueba_report.html
file? I would like to see what the histograms that didn't fit look like. It seems to be a tiny dataset.Yes, that is. It is a small dataset 25,770,300pb. I have sent email. Regards.