[maker-devel] maker dying on a contig

[Jeremy Semeiks]

Hi,

I'm trying to annotate a mammalian genome with maker-2.26-beta. I have
~36,000 contigs, and per the master log maker FINISHED all of them
except one (scaffold_10105, ~60 kbp, not obviously weird) on the first
run. It didn't report ERROR for that contig in the master log, but it
did output two DIED lines in the contig's run.log and then just hung
for a week until I killed it.

I reran maker on just that contig by deleting the START line from the
master log. maker again died on that contig.

I attach the relevant part of the stderr stream; the rest was just
"--Next Contig--"-type lines. Any ideas?

A related question. Is deleting lines in the master log, as I did
here, the best way to get maker to rerun on just a few contigs? I
often find myself needing to do this, sometimes because of ERROR lines
or other assumed quirks in maker and sometimes just because I needed
to pause a big run for a while. One disadvantage is that when I
restart, maker needs to manually scan over many completed contigs,
which takes a while.

(I'd think the best solution would be for maker to automatically
recognize whether it's really currently running on contigs marked
STARTED but not FINISHED. It doesn't seem to do this now, but I
realize that might be hard to implement.)

Thanks,
Jeremy
Grad student, Grishin lab
UT Southwestern, Dallas TX
510.384.8959
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