<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">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. <br class=""><div><br class=""></div><div>—Carson</div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Sep 6, 2021, at 2:50 PM, Adam Stuckert <<a href="mailto:stuckerta@gmail.com" class="">stuckerta@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi,<div class=""><br class=""></div><div class="">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 class=""><br class="">#---------------------------------------------------------------------<br class="">Now starting the contig!!<br class="">SeqID: P_RNA_scaffold_115<br class="">Length: 2076116<br class="">#---------------------------------------------------------------------<br class=""><br class=""><br class="">setting up GFF3 output and fasta chunks<br class="">doing repeat masking<br class=""><br class="">------------- EXCEPTION: Bio::Root::Exception -------------<br class="">MSG: Did not specify a Hit End or Hit Begin<br class="">STACK: Error::throw<br class="">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 class="">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 class="">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 class="">STACK: repeat_mask_seq::separate_types /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/<a href="http://repeat_mask_seq.pm:307/" class="">repeat_mask_seq.pm:307</a><br class="">STACK: repeat_mask_seq::mask_chunk /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/<a href="http://repeat_mask_seq.pm:191/" class="">repeat_mask_seq.pm:191</a><br class="">STACK: Process::MpiChunk::_go /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiChunk.pm:762<br class="">STACK: Process::MpiChunk::run /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiChunk.pm:340<br class="">STACK: Process::MpiChunk::run_all /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiChunk.pm:356<br class="">STACK: Process::MpiTiers::run_all /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiTiers.pm:287<br class="">STACK: Process::MpiTiers::run_all /mnt/oldhome/macmaneslab/macmanes/test/maker/bin/../lib/Process/MpiTiers.pm:287<br class="">STACK: /mnt/lustre/macmaneslab/macmanes/test/maker/bin/maker:679<br class="">-----------------------------------------------------------<br class="">--> rank=NA, hostname=node143.rcchpc<br class="">ERROR: Failed while doing repeat masking<br class="">ERROR: Chunk failed at level:0, tier_type:1<br class="">FAILED CONTIG:P_RNA_scaffold_54<br class=""><br class="">ERROR: Chunk failed at level:2, tier_type:0<br class="">FAILED CONTIG:P_RNA_scaffold_54<br class=""><br class="">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 class=""><br class="">Any suggestions? <br class=""><br class="">Thanks,<br class="">Adam<div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class=""></div></div></div></div></div>
<span id="cid:f_kt94b0z70"><rm.500lines.gff></span>_______________________________________________<br class="">maker-devel mailing list<br class=""><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class="">http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org<br class=""></div></blockquote></div><br class=""></body></html>