Greetings I'm a PhD student, working on visualization of synteny across genomes of strains of the same species (12 different synteny plots), and one synteny across different species genomes (up to 35 species). The synima pipeline is great and works to produce the plots.
In the third step, which establishes the orthology, I'm using the orthofinder script; I noticed that In some analyses, despite the orthology being established the analysis doesn't finish properly and there is missing information.
[proper orthofinder analysis]
[error orthofinder analysis]
I don't have the log from each analysis, and as far as I remember, the failed analysis always has some warning with one or more Orthogroup gene trees, but no other information is given.
Has anyone had the same problem or know how to identify the problem or have any ideas on how to avoid this issue?
Thanks in advance.
Greetings I'm a PhD student, working on visualization of synteny across genomes of strains of the same species (12 different synteny plots), and one synteny across different species genomes (up to 35 species). The synima pipeline is great and works to produce the plots.
In the third step, which establishes the orthology, I'm using the orthofinder script; I noticed that In some analyses, despite the orthology being established the analysis doesn't finish properly and there is missing information.
[proper orthofinder analysis]
[error orthofinder analysis]
I don't have the log from each analysis, and as far as I remember, the failed analysis always has some warning with one or more Orthogroup gene trees, but no other information is given.
Has anyone had the same problem or know how to identify the problem or have any ideas on how to avoid this issue?
Thanks in advance.