I have been running Maker2 for my genome annotation. I finished first round of the run with only ESTs and proteins (from other species) as evidence. While running the second run using the .hmm file produced from snap, I exceeded the run time and the program crashed. It was during the final stage and this is how the error log looks like.
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
=>> PBS: job killed: walltime 540041 exceeded limit 540000
mpiexec: killing job..
I would like to know if it's possible to re-run maker with the same settings, to save time? (ie., does it start from the same point it crashed) Or do I have to start over from the scratch?