<div dir="ltr">Hi,<div><br></div><div>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:<br><br>#---------------------------------------------------------------------<br>Now starting the contig!!<br>SeqID: P_RNA_scaffold_115<br>Length: 2076116<br>#---------------------------------------------------------------------<br><br><br>setting up GFF3 output and fasta chunks<br>doing repeat masking<br><br>------------- EXCEPTION: Bio::Root::Exception -------------<br>MSG: Did not specify a Hit End or Hit Begin<br>STACK: Error::throw<br>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<br>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<br>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<br>STACK: repeat_mask_seq::separate_types /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/<a href="http://repeat_mask_seq.pm:307">repeat_mask_seq.pm:307</a><br>STACK: repeat_mask_seq::mask_chunk /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/<a href="http://repeat_mask_seq.pm:191">repeat_mask_seq.pm:191</a><br>STACK: Process::MpiChunk::_go /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiChunk.pm:762<br>STACK: Process::MpiChunk::run /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiChunk.pm:340<br>STACK: Process::MpiChunk::run_all /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiChunk.pm:356<br>STACK: Process::MpiTiers::run_all /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiTiers.pm:287<br>STACK: Process::MpiTiers::run_all /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiTiers.pm:287<br>STACK: /mnt/lustre/macmaneslab/macmanes/test/maker/bin/maker:679<br>-----------------------------------------------------------<br>--> rank=NA, hostname=node143.rcchpc<br>ERROR: Failed while doing repeat masking<br>ERROR: Chunk failed at level:0, tier_type:1<br>FAILED CONTIG:P_RNA_scaffold_54<br><br>ERROR: Chunk failed at level:2, tier_type:0<br>FAILED CONTIG:P_RNA_scaffold_54<br><br>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.<br><br>Any suggestions? <br><br>Thanks,<br>Adam<div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div></div></div></div></div></div>