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Problems with database creation #2
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Hi Maria The "full" and "profiles" options should be explained in the paper, basically it's whether you want an orthogroup to be represented by all is members in the diamond database (full) or just selected representatives (profile). I'd recommend trying full to start with. Best wishes |
Dear David, Also then i ran python test_msa_grafter_epa.py I got the following error and for python test_utils.py it is the same mistake. Best wishes, |
Hello |
@Luponsky no, I used local BLAST and constructed phylogenetic trees to find needed orthologous groups. |
Hi David!
I'm trying to run python create_shoot_db.py command to my local data. The code looks like this:
python create_shoot_db.py /mnt/c/Users/uzunm/mydata/OrthoFinder/Results_Mar30_5/
I got the comment "Args: input_directory [full,profiles]."
What does it mean? How can I fix this? OrthoFinder directory contains many subdirectories. Should I give the path to the entire directory or to a specific subdirectory?
Kind regards,
Maria
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