ValueError: n_components=3 must be between 0 and min

[YuChrming]

Dear Writer !
Thanks for your useful pipline, but I meet an error when use SubPhaser.
My command
subphaser -i groups_genome.fasta -c groups_sg.config
My configue file

But I have the error

What's wrong with me ?

[zhangrengang]

@YuChrming,
Your genome has too few differential kmers between subgenomes. It may be artifactual or natural. My suggestions (refer to the Supplementary Material):

1. Check the HiC contact map whether there are too many switch errors between subgenomes. If not, it is natural.
2. If natural, it may be because 1) there are too many recombinations between subgenomes after hybridization, or 2) their progenitors are too close (possible autopolyploid) to distinguish. In these cases, subgenome phasing is meaningless and subphaser will not work.
3. Another possibility is that your genome is hybridizated from an autotetraploid and a distinct diploid, and you can try -baseline -1 to compare the most and the least abundance of kmers.

[YuChrming]

Thanks for your quick reply!
My Hi-C heatmap is not bad, at least in my opinion.

Then, I try -baseline -1 but the error is still.

May it is highly homologous? But it should be an allotriploid evidenced by many literatures.

[zhangrengang]

1. Have you removed the check point files (tmp/*ok) before re-run or used the -overwrite option?
2. What are the evidences for allo?