SubPhaser

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三倍体基因组

1

 老师，您好 三倍体基因组划分成这样了，单套17条，还能有改善吗

liufuyan2016

sg.config configuration (The homology of the de novo assembled genome is not known)

24

Hello, thank you very much for your SubPhaser software, which is very useful for genotyping. I used HIFI and HIC to assemble the genome of Fragaria x ananassa but I...

hushaoqiang

IndexError: index -1 is out of bounds for axis 0 with size 0

7

Hi, Thanks for developing the tool. I tried the example of ginger and successfully procressed. But When I used my own triploid genome (3n=63), I met an error. My config...

yilunhuangyue

ValueError: n_components=3 must be between 0 and min

3

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...

YuChrming

Division by zero when trying to build trees?

12

Hi, when running SubPhaser i get the following error: ``` Traceback (most recent call last): File "/home/531734/.conda/envs/SubPhaser/bin/subphaser", line 33, in sys.exit(load_entry_point('subphaser==1.2.5', 'console_scripts', 'subphaser')()) File "/home/531734/.conda/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.5-py3.8.egg/subphaser/__main__.py", line 779, in main pipeline.run()...

mrmrwinter

亚基因组分析

2

张老师， 您好！正在用subphaser分一个异源四倍体的AB亚基因组，得到初步结果，请您帮忙看看。装出来的基因组共22条染色体，在subphaser分析后，一组为12条，另一组10条，目前这里比较迷惑，请您指点。结果如下图：    

zhdang

cannot allocate memory

13

Hi, Thanks a lot for the very nice tool! I am trying to phase the subgenomes from this hexaploid haplotype-phased genome (9Gb), but somehow I always get stuck with the...

dabitz

ValueError: 0 kmer with fold > 2. Please reset the filter options.

1

When I analyze using the default parameters, the following error occurs. What should I set the kmer parameters to? 23-12-30 15:24:20 [INFO] After filtering, remained 0 (0.00%) differential (freq >=...

z626093820

No differential kmers

2

Hi, I am trying to use the SubPhaser to phase the subgenomes of my species. However, after filtering differential kmers, no differential kmers were remained. I used parameter of this...

xychen233

Unbalanced of chromosomes number and differential kmers number among subgenomes

1

Hi~, I have got a whole new set of problems now:  there is abnormally few subgenome-specific kmers in one of subgenomes, and the numbers of assigned chromosomes among subgenomes...

xingjianfeng100