"*run_*" in directory name

[jamiemcg]

Having "*run_*" in the BUSCO output directory name causes an error (e.g. BUSCO5_rerun_XYZ_output)

https://github.com/jamiemcg/BUSCO_phylogenomics/blob/0589f6ce883c3ebfa3b7521339d8caaf7f8bc526/count_buscos.py#L44-L49

(It looks for BUSCO sequences in the "logs" directory as it thinks it is the run directory, e.g. "run_alveolata_odb10")

Try something like this to fix:

         if isdir(i):
             for j in listdir(i):
                 k = join(i, j)
                 if isdir(k) and "run_" in j:
                     busco_samples.append(k)
                     busco_sample_names.append(basename(i))