Hi Carson,
Looking at the progress more carefully, I learned that some query and database combinations cause tblastx to run forever. Typically, the tblastx search ends in reasonable times (a few hours maximum), but for those, it takes days ( and still running ) to search the 100 kb query against a 50 Mb database. And all CPUs are trapped by these searches, making MAKER to never finish.
Would it be possible to skip tblastx search for these queries + databases? I have intermediate files from a previous MAKER run produced with a smaller size of databases, so I attempted to copy some of these files into the current run folders. For instance, for atg000169l.12.Solanacea%2Ecds%2Efa.tblastx.temp_dir that causes the issue,
I first copied atg000169l.12.Solanacea%2Ecds%2Efa.tblastx from the previous run into the proper directory and deleted
atg000169l.12.Solanacea%2Ecds%2Efa.tblastx.temp_dir.
Then I modified run.log.child.12 to include FINISHED SH1353.alternative.noPlasmid.maker.output/SH1353.alternative.noPlasmid_datastore/42/CC/atg000169l//theVoid.atg000169l/1/atg000169l.12.Solanacea%2Ecds%2Efa.tblastx
However, it seems like MAKER still starts over from tblastx. I have a small number of contigs left, so manually working around this is feasible. Would there be a way to do this?
Thank you for your help!
Kyungyong