script execution never ends

[simleopold]

Hi,

I'm using jellyfish and I ran the dedicated script.

L=$(smudgeplot.py cutoff 21mer_no_cut.histo L)
U=$(smudgeplot.py cutoff 21mer_no_cut.histo U)
echo $L $U 
jellyfish dump -c -L $L -U $U Prymnesium_kmer.jf | smudgeplot.py hetkmers -o kmer_pairs

The problem is it never ends and I don't know why.

Thanks for your help,

[KamilSJaron]

Hi, what does echo $L $U return? Did you try to look at the k-mer spectra?

THat is usually because there are too many errors in the dump for such small genomes as yours.

[simleopold]

It returns 10 and 310 respectively. I did not look at the k-mer spectra, I will try. Thanks for your help