IndexError: index -1 is out of bounds for axis 0 with size 0 about subphaser HOT 7 OPEN

Can you show me the whole log and the plots produced by subphaser? I suspect that the genome is not well phased.

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log.txt

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As clearly shown by the results, the subgenomes are not well assigned, because there are 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.

So many chromosomes may also be an issue. You can have a try to reduce the number of homeologous chromosome sets by setting the config like:

1 2 3
...
13 14 15
16
17
18
...
75
76
77

Remove check point files by rm tmp/*ok before re-runing to avoid confusing.

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Thank you for your quick reply. I will take a try

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