Configuration file

[yliasolom]

Hello! How can I create Configuration file for genome?

[zhangrengang]

@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.

[yliasolom]

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

[zhangrengang]

@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.