[maker-devel] Maker jobs hanging

[Greg Taylor]

Hello,
 I'm having a problem with Maker_2.28 jobs hanging. I am annotating a 3Gb genome with predictors SNAP and Genemark, and using ABySS assembled RNA-seq data. To do this I am using 480 processors on our local cluster. Once a run begins, 479 contigs are started, as noted in the *_master_datastore_index.log file, the standard error log for the whole job looks normal, as do the run.log and run.log.child.0 for the daughter processes. This seems to be sequence dependent, as re-running contigs that hang doesn't help, the same contigs will always hang. I'm still looking into this myself, but it seems most if not all the jobs are stuck at the Blastx stage. If you have any suggestions, your help would be greatly appreciated.

sincerely,
Greg Taylor