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IndexError: cannot do a non-empty take from an empty axes. #15
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Are your final assignments (>With a smaller number of assignments, SubPhaser successfully completed in the same genome with a smaller number of homologous chromosome assignments) correct? |
Sorry, my writing was a little strange because I wrote the above comment just before I went to bed last night. SubPhaser was completed, but the final assignments didn't seem to be correct (given our data on the synteny and subgenome dominance of this decaploid plant). On the other hand, we have no evidence that this species is an allopolyploid, so the fact that SubPhaser does not phase well may mean autopolyploidy or that the ancestral species were very similar to each other. |
For decaploid, it is hard to phase as there may be 2-5 subgenomes in fact and it maybe very complicated in nature. I have successfully phased upon to octoploid with 4 subgenomes. As there are no more priors, you may have to make more tries.
And |
Thank you, I started trying it. I thought the above error occurred because SubPhaser assigned all scaffolds to SG1, but I got the same error with
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The error is because there are none subgenome-specific LTR-RTs identified (the phasing step maybe failed). |
Yes, too few differential kmers. |
Should I close this issue if the IndexError is intended? |
OK. I will change it to "warning". |
I am closing this issue as the bug seems to have been fixed. Thank you! |
Hi, I got the following error with my dataset when I was trying to pre-assign all 40 chromosomes to 2 subgenomes. Apparently, SubPhaser re-assigned all chromosomes to SG1. With a smaller number of assignments, SubPhaser successfully completed in the same genome with a smaller number of homologous chromosome assignments, as you suggested in #7.
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