[maker-devel] Issues including Repeat Masker gff in Maker runs

[Carson Holt]

A couple of things. First let MAKER run RepeatMasker.  Don’t provide the RepeatMasker GFF as input to MAKER. The file you sent is GFF version 2 for example which is not backwards compatible with GFF version 3. Second use the latest versions of MAKER2 or MAKER3.  There is an issue with RepeatMasker sometimes producing start/end coordinates that are 0 or even negative numbers.  The current releases of MAKER2/3 know how to find and fix invalid coordinate features. 

—Carson


> On Sep 6, 2021, at 2:50 PM, Adam Stuckert <stuckerta at gmail.com> wrote:
> 
> Hi,
> 
> I have been working on this problem for a while now, but can't seem to come up with a solution despite extensive searching. When I include a repeat masker gff, it always fails with messages like this:
> 
> #---------------------------------------------------------------------
> Now starting the contig!!
> SeqID: P_RNA_scaffold_115
> Length: 2076116
> #---------------------------------------------------------------------
> 
> 
> 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 /mnt/oldhome/software/anaconda/colsa/envs/maker-3.01.02/lib/perl5/site_perl/5.22.0/Bio/Root/Root.pm:447
> STACK: Bio::Search::HSP::GenericHSP::_subject_seq_feature /mnt/oldhome/software/anaconda/colsa/envs/maker-3.01.02/lib/perl5/site_perl/5.22.0/Bio/Search/HSP/GenericHSP.pm:1603
> STACK: Bio::Search::HSP::GenericHSP::hit /mnt/oldhome/software/anaconda/colsa/envs/maker-3.01.02/lib/perl5/site_perl/5.22.0/Bio/Search/HSP/GenericHSP.pm:987
> STACK: repeat_mask_seq::separate_types /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/repeat_mask_seq.pm:307 <http://repeat_mask_seq.pm:307/>
> STACK: repeat_mask_seq::mask_chunk /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/repeat_mask_seq.pm:191 <http://repeat_mask_seq.pm:191/>
> STACK: Process::MpiChunk::_go /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiChunk.pm:762
> STACK: Process::MpiChunk::run /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiChunk.pm:340
> STACK: Process::MpiChunk::run_all /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiChunk.pm:356
> STACK: Process::MpiTiers::run_all /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiTiers.pm:287
> STACK: Process::MpiTiers::run_all /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiTiers.pm:287
> STACK: /mnt/lustre/macmaneslab/macmanes/test/maker/bin/maker:679
> -----------------------------------------------------------
> --> rank=NA, hostname=node143.rcchpc
> ERROR: Failed while doing repeat masking
> ERROR: Chunk failed at level:0, tier_type:1
> FAILED CONTIG:P_RNA_scaffold_54
> 
> ERROR: Chunk failed at level:2, tier_type:0
> FAILED CONTIG:P_RNA_scaffold_54
> 
> I have tried a number of ways to modify the output of RepeatMasker to fit with Maker's expectation, and to me, the gff looks fine (see attached, which is the first 500 lines of a repeatmasker.gff I've used. Note it says "similarity" for hit type, but I've also changed the gff to only have "match_part" and had the same issue). I have had this issue across multiple clusters.
> 
> Any suggestions? 
> 
> Thanks,
> Adam
> <rm.500lines.gff>_______________________________________________
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