<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Dear Carson,</div><div class=""><br class=""></div>I got exactly the same problem as Ole Kristian Torresen.<div class=""><div class=""><b class="">substr outside of string at /projects/cees/bin/maker/maker-3.01.1/bin/../lib/PhatHit_utils.pm line 850.</b></div><div class="">I also tried with the version 3.00.0 and got the same problem.</div><div class=""><br class=""></div><div class="">My run:</div><div class="">I was using gff3 alignements as gff ESTs, proteins and activating repeat masking and trna.<br class=""><div class=""><br class=""></div><div class="">The code line in <b class="">PhatHit_utils.pm</b> is the following:</div><div class=""> my $transcript_seq = maker::auto_annotator::get_transcript_seq($hit, $seq); <b style="font-family: Calibri;" class=""># few line before</b></div><div class=""> …..</div><div class=""><div class=""><font face="Calibri" class=""> <span class="Apple-tab-span" style="white-space:pre"> </span>#fix stop codon by walking downstream </font></div><div class=""><font face="Calibri" class=""> <span class="Apple-tab-span" style="white-space:pre"> </span>my $has_stop = $tM->is_ter_codon(substr($transcript_seq, $end-1-3, 3)); <b class=""># <= line 850</b></font></div></div><div class=""><br class=""></div><div class="">So, I relaunched using the —debug option but didn’t find anything useful.</div><div class=""><br class=""></div><div class="">Consequently I modified the code to display the $transcript_seq object.</div><div class="">I joined the log were you can see the printed object from line 10955. </div><div class=""><div class="">I also printed the size of the sequence (length(<span style="font-family: Calibri;" class="">$transcript_seq</span>)) and <span style="font-family: Calibri;" class="">$end</span>.</div><div class="">We can see that it crashes because the sequence is 1369 bp long and we try to extract a stop codon from position 1372 (1376-1-3). </div></div><div class=""><div class=""></div></div></div></div></body></html>