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

[Jacques Dainat]

I got the same error as previously mentioned by Greer Dolby the 15th of June.
I share my experience hopping it could help to catch the problem.

.processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
Died at /sw/bioinfo/maker/3.01.02-beta-OMPI-perl5.16/bin/../lib/maker/auto_annotator.pm line 1774.
--> rank=36, hostname=bnode-06
ERROR: Failed while choosing best annotation set
ERROR: Chunk failed at level:4, tier_type:4
FAILED CONTIG:@000261F|arrow|arrow

I’m using:
- MAKER 3.01.02-beta
- openmpi 2.1.2
- perl 5.16.3
- BioPerl 1.6.922
- Exonerate 2.4
- blast+ 2.7.1
- evm 1.1.1
- genemark 4.3
- augustus 2.7
- repeat masker 4.0.3

As externaI data I use proteins in fasta format, transcriptomes in fasta format and transcriptomes in gff format.
I have  first run MAKER with est2genome and protein2genome set to 1 and single_exon=1 (important for the bug it seems). => it has worked fine
Then I have run the same data with est2genome and protein2genome set to 0 and genemark, snap, augustus and evm activated and still single_exon=1 => it has worked fine.
I wanted to give a last try with the same parameters as the previous run but put single_exon=0 => 2 contigs  crash on the 6000 contigs my assembly has

I have extracted the sequence and relaunched MAKER apart it in a fresh folder. I have exactly the same error.

Best regards,

Jacques

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