[maker-devel] Best annotation set failure (auto_annotator.pm line 1774)

[Greer Dolby]

Hello,

I’m de novo annotating a second-generation genome and I have a handful of scaffolds that keep failing while choosing the best annotation set (errors below). To my knowledge there is anything wrong with the scaffolds themselves and the others have run fine. Looking at the VOID folder for the failed contigs for different runs, they appear to fail at different chunks but always with these two errors. I’m running 30 cores with MPICH2 on a private server. Any suggestions? Thanks!

Best,
Greer

^^^^^^^^^^^^^^^^^^^^^^^^^^EXAMPLE 1
 ...processing 8 of 12
total clusters:44 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:44 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 9 of 12
 ...processing 2 of 4
 ...processing 3 of 4
total clusters:44 now processing 0
 ...processing 10 of 12
 ...processing 0 of 67
 ...processing 1 of 67
ERROR: Chunk failed at level:6, tier_type:0
 ...processing 2 of 67
FAILED CONTIG:ScCC6lQ_38465;HRSCAF=64658

^^^^^^^^^^^^^^^^^^^^^^^^^^EXAMPLE 2
 ...processing 9 of 298
 ...processing 8 of 81
 ...processing 11 of 202
 ...processing 13 of 20
 ...processing 10 of 298
 ...processing 9 of 81
 ...processing 10 of 81
 ...processing 18 of 123
 ...processing 14 of 20
 ...processing 17 of 54
 ...processing 18 of 54
 ...processing 37 of 164
 ...processing 20 of 254
Died at /home/jcornel3/tools/maker/bin/../lib/maker/auto_annotator.pm line 1774.
--> rank=17, hostname=omega
ERROR: Failed while choosing best annotation set
ERROR: Chunk failed at level:4, tier_type:4
FAILED CONTIG:ScCC6lQ_16796;HRSCAF=38896
_________________________________
Greer Dolby, PhD
Postdoctoral Research Scholar
SoLS, Arizona State U.
office: LSE 313, 480.965.7456
website <http://www.greerdolby.org/> | twitter <https://twitter.com/gadolby>
Kusumi Lab <http://kusumi.lab.asu.edu/>
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