[maker-devel] Questions about repeat masking in MAKER

[Ran Zhang]

Hi,

I am using maker to do repeat masking and genome annotation. So far I have assembly, est and protein evidence. What I did is use maker to initialized three files and only edit the maker_opts.ctl. I put the genome, est and proteins. Also I changed the est2geome=1 and protein2gemone=1. But what I got is always wrong. I used the high performance cluster in our university and it is already installed MPI with maker. Error showed like this .
I am a little confused about that should maker cannot do repeat masking automatically for me? I have to use RepeatModeler/RepeatMasker to do that first then use maker and skip the repeat masking? Or I have to make the specific repeat library and this is also a required file (although the tutorial said only 3 files required).

Thanks a lot!

Ran



setting up GFF3 output and fasta chunks
parseTagData: ID field not to EMBL spec "SNAP-OL2 repeatmasker; DNA; ???;  BP.
" from DE   RepbaseID: SNAP-OL2XX

 at /usr/local/apps/maker/v2.31.10/exe/RepeatMasker/RepeatMasker line 7611.
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_joy_Oe; /usr/local/apps/maker/v2.31.10/exe/RepeatMasker/RepeatMasker /gpfs_common/share03/bonelllin/rzhang12/maker1/f2.renamed.maker.output/f2.renamed_datastore/04/3F/bviridis90138//theVoid.bviridis90138/0/bviridis90138.0.all.rb -species all -dir /gpfs_common/share03/bonelllin/rzhang12/maker1/f2.renamed.maker.output/f2.renamed_datastore/04/3F/bviridis90138//theVoid.bviridis90138/0 -pa 1
#-------------------------------#
parseTagData: ID field not to EMBL spec "SNAP-OL2 repeatmasker; DNA; ???;  BP.
" from DE   RepbaseID: SNAP-OL2XX

 at /usr/local/apps/maker/v2.31.10/exe/RepeatMasker/RepeatMasker line 7611.
ERROR: RepeatMasker failed
--> rank=12, hostname=n3i4-13
ERROR: Failed while doing repeat masking
ERROR: Chunk failed at level:0, tier_type:1
FAILED CONTIG:bviridis90124

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:bviridis90124

parseTagData: ID field not to EMBL spec "SNAP-OL2 repeatmasker; DNA; ???;  BP.
" from DE   RepbaseID: SNAP-OL2XX

 at /usr/local/apps/maker/v2.31.10/exe/RepeatMasker/RepeatMasker line 7611.
parseTagData: ID field not to EMBL spec "SNAP-OL2 repeatmasker; DNA; ???;  BP.
" from DE   RepbaseID: SNAP-OL2XX

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