Restart question
I was running busco on multiple threads but after a fairly short time, I was getting a threading error (something about blocking and a new thread being unable to be opened; occurred during the running of Augustus). I tried lowering the thread number and restarting, and it went directly to the augustus step, however it appears to restart the entire Augustus phase, ignoring any already generated Augustus results, and then crashed about the same place - roughly 10-15% of the Augustus commands that would have run eventually completed. Rather than just reduce the number of threads to 1, I decided to try another tack, and ran the remaining Augustus commands outside of busco, using/mimicking the busco files as input/output so that eventually I had all the Augustus jobs completed and the output placed in "my_busco_dir/augustus_output/predicted_genes." I was hoping that if I did this then tried "run_busco.py --restart"that it would see that the Augustus phase was complete and move on to the next step. This doesn't seem to be happening however. Instead it seems like it wants to go all the way back to the tblastn step (i.e. start the whole run over), even though my tblastn output is still present in "my_busco_dir/blast_output." I am assuming there is not a second round of tblastn that should be occurring for some reason. If my assumption is correct, is there something I can do to get/trick run_busco.py to restart the run at the post-Augustus phase?
Thanks,
John Martinson