[maker-devel] Maker problem

[Jan FABI]

Dear Maker team

I am experiencing a problem while running maker and cannot find a solution
to it online.

I am running maker on a new genome, using BRAKER trained models for
Augustus and GeneMark. This was successful and performed as expected,
except for one contig where an error was encountered.

This error occurs during Augustus and seems to have something to do with
intron models. I have made sure that the input fasta does not contain
characters other than ATCGN or contains "windows"/non-UNIX carriage
returns.

I include the relevant portion of the log below. Could you help me
determine the cause of this error.



setting up GFF3 output and fasta chunks
preparing ab-inits
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus
--species=Np_2017_braker --UTR=off
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0 >
/tmp/maker_bQo5Oc/NODE_1040_length_26483_cov_27%2E125137.abinit_masked.0.Np_2017_braker.augustus
#-------------------------------#
Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

Sampling error in intron model. state=37 base=26570

/home/xxx/Desktop/programs/augustus-3.2.3/bin/augustus: ERROR
    Tried to sample from empty list.

ERROR: Augustus failed
--> rank=NA, hostname=xxx-VirtualBox
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:NODE_1040_length_26483_cov_27.125137

-- 
Regards
Jan Nagel
----------------------------------------------------------------------
PhD Genetics student
Department of Genetics
Forestry and Agricultural Biotechnology Institute (FABI)
FABI 1, Room 1-55
University of Pretoria
74 Lunnon Rd. Hillcrest
0002
Gauteng Province
South Africa

Email : jan.nagel at fabi.up.ac.za

Website: http://www.fabinet.up.ac.za/index.php/people-profile?profile=961

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