[maker-devel] Question about maker. Maker2 failed

[Carson Holt]

It is probably the formating of the models provided. There is something wrong with them. They must be match/match_part two level feature for rm_gff. You can send us the file, and I can take a look if it helps.

—Carson


> On May 5, 2020, at 2:41 PM, 祖尧刘 <zuyao.liu.0910 at gmail.com> wrote:
> 
> Hi maker developer,
> 
> I'm using maker 2 to annotate a vertebrate genome.
> When I try to provide rm_gff file, it always fails.
> Here is log:
> Now starting the contig!!
> SeqID: chr_XXII
> Length: 12689475
> #---------------------------------------------------------------------
> 
> 
> setting up GFF3 output and fasta chunks
> doing repeat masking
> 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Did not specify a Hit End or Hit Begin
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/lib/site_perl/5.26.2/Bio/Root/Root.pm:449
> STACK: Bio::Search::HSP::GenericHSP::_subject_seq_feature /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/lib/site_perl/5.26.2/Bio/Search/HSP/GenericHSP.pm:1604
> STACK: Bio::Search::HSP::GenericHSP::hit /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/lib/site_perl/5.26.2/Bio/Search/HSP/GenericHSP.pm:988
> STACK: repeat_mask_seq::separate_types /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/repeat_mask_seq.pm:307 <http://repeat_mask_seq.pm:307/>
> STACK: repeat_mask_seq::mask_chunk /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/repeat_mask_seq.pm:191 <http://repeat_mask_seq.pm:191/>
> STACK: Process::MpiChunk::_go /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiChunk.pm:763
> STACK: Process::MpiChunk::run /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiChunk.pm:341
> STACK: Process::MpiChunk::run_all /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiChunk.pm:357
> STACK: Process::MpiTiers::run_all /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiTiers.pm:287
> STACK: Process::MpiTiers::run_all /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiTiers.pm:287
> STACK: /home/ubelix/iee/zl19g775/miniconda3/envs/maker/bin/maker:689
> -----------------------------------------------------------
> --> rank=NA, hostname=submit02.ubelix.unibe.ch <http://submit02.ubelix.unibe.ch/>
> ERROR: Failed while doing repeat masking
> ERROR: Chunk failed at level:0, tier_type:1
> FAILED CONTIG:chr_XXII
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:chr_XXII
> 
> examining contents of the fasta file and run log
> 
> 
> 
> I also searched the google group and tried update my bioperl to 1.7.7 the latest version, but it didn't help.
> 
> Could you please help me?
> 
> Thanks a lot.
> 
> Zuyao
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