[maker-devel] Fwd: all scaffolds failed

[Sunny Sun]

Hi,
I am trying to annotate with Maker a set of 7k scaffolds with a genome size
of 160Mb. The first run returned 10% of scaffolds FAILED and the remaining
FINISHED but I didn't get the protein or transcripts fasta files so I
modified the configuration files accordingly and I am rerunning the
analysis. So far, all the scaffolds are failing, in the error.log the only
error I see is of this type for all scaffolds:

error in file format, /tmp/I16VH9JkXG/Q3Pi3DDTOZ_mod
ERROR: GeneMark Failed
ERROR: Genemark failed
--> rank=NA, hostname=sol
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:scaffold_6

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scaffold_6

examining contents of the fasta file and run log

which doesn't tell me much. I attached the config files. Can someone see
what is wrong?

Thanks
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