Maker2 restart after crash

Question

[sukyi]

Hi,

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.

scoring....decoding.10.20.30.40.50.60.70.80.90.100 done

deleted:0 genes

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

SIGTERM received

SIGTERM received

SIGTERM received

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?

Thanks!

Answer 1

[GenoMax]

Unless check pointing is included in MAKER2 you will have to re-start the job. Looks like your job ran out of time.

[sukyi]

This is what I need to know- If there is any checkpoint included. I don't see it anywhere in the manual. Except for the -a (again) option that sounds similar but not clear enough.

[GenoMax]

See this message and also this one from MAKER-devel list seem to indicate that MAKER does have checkpointing.

[sukyi]

Awesome! I somehow seemed to miss it. Thank you, genomax.