[maker-devel] Question about maker. Maker2 failed

[祖尧刘]

Hi maker developers

I'm using maker 2 to annotate a fish genome.

When I try to provide rm_gff file, it always fails.

Here is log:

collecting blastx repeatmasking
doing repeat masking
processing all repeats
deleted:0 hits
in cluster::shadow_cluster...
Died at /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm line 188.
--> rank=23, hostname=hnode48
ERROR: Failed while processing all repeats
ERROR: Chunk failed at level:3, tier_type:1
FAILED CONTIG:chr_XXIII

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

I use maker 2.3.10 with repeatmasker 4.0.9.

I saw someone got this error as well and I followed the solutions.

I  tried update to blast 2.9.0, rmblast 2.9.0,bioperl1.7.7 and also checked rm gff file with gff3 validator. But the error still existed.

Do you have any suggestions?

Thanks a lot for your help.

[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.l...@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

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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