piamer
commented
3 weeks ago Hi, a quick update - I've tried with a newer version of ODP from the github and am encountering the same error (now line 372, but same text). So it isn't because I'm using an older version. Not sure what to do to fix this
Hiya!
I've been trying to run ODP, and am successfully generating the ALG plots, however whenever I try to run the #plot_sp_sp: True to generate synteny plots, I get this error: MissingInputException in line 289 of .../scripts/odp: Missing input files for rule n_ways_reciprocal_best: (Bearing in mind I am running an older version of ODP, from the zenodo for Schultz et al 2023, so the error may not be on the same line in the current version)
I have run the exact same pipeline on the data from Schultz et al (2023), where I suiccessfully generated the sp_sp synteny, however on my own data this doesn't work. My config file parameters look like this:
num_permutations: 10000000 ignore_autobreaks: True # Skip steps to find breaks in synteny blocks diamond_or_blastp: "diamond" # diamond or blastp plot_LGs: True # Plot the ALGs based on the installed databases plot_sp_sp: True # Plot the synteny between two species, if False just generates .rbh files
I have also (unsuccessfully) tried with blastp instead of diamond, and without num_permutations. I'm using diamond vers 2.1.9.