Question about maker. Maker2 failed

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Question about maker. Maker2 failed

祖尧刘

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
STACK: repeat_mask_seq::mask_chunk /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/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
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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Re: Question about maker. Maker2 failed

Carson Holt-2
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 <[hidden email]> 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
STACK: repeat_mask_seq::mask_chunk /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/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
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
_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org


_______________________________________________
maker-devel mailing list
[hidden email]
http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org