Comments (3)
@yliasolom If you do not have any priors about the homoeologous chromosome relationshipes, you need to identify them using genome alignments or syntenic analyses. Refer to the user guide in https://nph.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fnph.18173&file=nph18173-sup-0001-SupInfo.pdf.
Examples of Configuration file can be fould in https://github.com/zhangrengang/SubPhaser#inputs or https://github.com/zhangrengang/SubPhaser/tree/master/example_data.
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I created for _Avena_longiglumis this file : https://www.ncbi.nlm.nih.gov/assembly/GCA_023614385.1
Chr1A|OU342747.1
Chr2A|OU342748.1
Chr3A|OU342749.1
Chr4A|OU342750.1
Chr5A|OU342751.1
Chr6A|OU342752.1
Chr7A|OU342753.1
But I had problems with singletons.... I suppose I made a wrong configuration file...
How can I fix it?
Traceback (most recent call last):
File "/home/ysolomennikowa/miniconda3/envs/SubPhaser/bin/subphaser", line 33, in
sys.exit(load_entry_point('subphaser==1.2.5', 'console_scripts', 'subphaser')())
File "/home/ysolomennikowa/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.5-py3.8.egg/subphaser/main.py", line 784, in main
pipeline.run()
File "/home/ysolomennikowa/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.5-py3.8.egg/subphaser/main.py", line 414, in run
d_mat = dumps.filter(d_mat, lengths, self.sgs, outfig=histfig, #d_targets=d_targets,
File "/home/ysolomennikowa/miniconda3/envs/SubPhaser/lib/python3.8/site-packages/subphaser-1.2.5-py3.8.egg/subphaser/Jellyfish.py", line 479, in filter
raise ValueError('All singletons are not allowed')
ValueError: All singletons are not allowed
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@yliasolom Subphaser aims to polyploids/hybrids that have more than one subgenomes, but Avena_longiglumis is not polyploids/hybrids. It has only one (sub)genome.
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Related Issues (20)
- Error in os.link(figfile, dstfig) HOT 3
- IndexError: cannot do a non-empty take from an empty axes. HOT 10
- Failed to install SubPhaser HOT 9
- ModuleNotFoundError: No module named 'TEsorter' HOT 4
- The output subgenomes are not paired HOT 4
- Changing mutation rate HOT 1
- Invalid specifier: '>=3.6:' HOT 1
- Only one pair of homologous chromosomes were not phased HOT 5
- matplotlib raise RuntimeError ('Invalid DISPLAY variable') HOT 2
- Unbalanced of chromosomes number and differential kmers number among subgenomes HOT 1
- `TEsorter` cannot find `rexdb` in Singularity container HOT 3
- Singularity container fails if environmental variable `R_LIBS_USER` is set HOT 2
- No differential kmers HOT 2
- ValueError: All singletons are not allowed HOT 1
- ValueError: 0 kmer with fold > 2. Please reset the filter options. HOT 1
- cannot allocate memory HOT 13
- 亚基因组分析 HOT 2
- Getting location of subgenome specific TEs HOT 2
- Suggestion for specific settings to improve subphasing HOT 3
- kmer 13 or less gives a lot of broken pipe errors HOT 5
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