<div dir="ltr"><p style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">Hi maker developer,</p><p style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></p><p style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">I'm using maker 2 to annotate a vertebrate genome.</p><p style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">When I try to provide rm_gff file, it always fails.</p><p style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">Here is log:</p><p style="margin-top:0px;margin-bottom:0px;color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"></p><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">Now starting the contig!!</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">SeqID: chr_XXII</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">Length: 12689475</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">#---------------------------------------------------------------------</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">setting up GFF3 output and fasta chunks</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">doing repeat masking</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">------------- EXCEPTION: Bio::Root::Exception -------------</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">MSG: Did not specify a Hit End or Hit Begin</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: Error::throw</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: Bio::Root::Root::throw /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/lib/site_perl/5.26.2/Bio/Root/Root.pm:449</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">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</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">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</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: repeat_mask_seq::separate_types /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/<a href="http://repeat_mask_seq.pm:307">repeat_mask_seq.pm:307</a></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: repeat_mask_seq::mask_chunk /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/<a href="http://repeat_mask_seq.pm:191">repeat_mask_seq.pm:191</a></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: Process::MpiChunk::_go /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiChunk.pm:763</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: Process::MpiChunk::run /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiChunk.pm:341</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: Process::MpiChunk::run_all /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiChunk.pm:357</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: Process::MpiTiers::run_all /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiTiers.pm:287</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: Process::MpiTiers::run_all /gpfs/homefs/iee/zl19g775/miniconda3/envs/maker/bin/../lib/Process/MpiTiers.pm:287</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">STACK: /home/ubelix/iee/zl19g775/miniconda3/envs/maker/bin/maker:689</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">-----------------------------------------------------------</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">--> rank=NA, hostname=<a href="http://submit02.ubelix.unibe.ch">submit02.ubelix.unibe.ch</a></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">ERROR: Failed while doing repeat masking</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">ERROR: Chunk failed at level:0, tier_type:1</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">FAILED CONTIG:chr_XXII</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">ERROR: Chunk failed at level:2, tier_type:0</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">FAILED CONTIG:chr_XXII</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">examining contents of the fasta file and run log</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">I also searched the google group and tried update my bioperl to 1.7.7 the latest version, but it didn't help.</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">Could you please help me?</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">Thanks a lot.</div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px"><br></div><div style="color:rgb(0,0,0);font-family:Calibri,Helvetica,sans-serif,serif,EmojiFont;font-size:16px">Zuyao</div></div>