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

[Adam Stuckert]

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
STACK: repeat_mask_seq::mask_chunk
/mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/
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
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